Starting phenix.real_space_refine
on Thu Jul 24 04:41:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y0w_33552/07_2025/7y0w_33552_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y0w_33552/07_2025/7y0w_33552.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y0w_33552/07_2025/7y0w_33552.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y0w_33552/07_2025/7y0w_33552.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y0w_33552/07_2025/7y0w_33552_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y0w_33552/07_2025/7y0w_33552_neut.cif"
  }
  resolution = 3.42
  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      22      5.16       5
     C    3222      2.51       5
     N     853      2.21       5
     O     989      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5086
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 930
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 6, 'TRANS': 116}
    Chain: "B"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 826
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 927
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 927
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "L"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 817
          Classifications: {'peptide': 109}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    Chain: "R"
      Number of atoms: 1548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1548
          Classifications: {'peptide': 193}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "X"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 4.54, per 1000 atoms: 0.89
  Number of scatterers: 5086
  At special positions: 0
  Unit cell: (102.96, 91.52, 83.2, 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      22     16.00
     O     989      8.00
     N     853      7.00
     C    3222      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.06
    Simple disulfide: pdb=" SG  CYS R 391 " - pdb=" SG  CYS R 525 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG X   1 " - " NAG X   2 "
    BETA1-6
      " NAG X   1 " - " FUC X   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
  Time building additional restraints: 1.49
  Conformation dependent library (CDL) restraints added in 685.3 milliseconds
  

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1188

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 13 sheets defined
      5.7% alpha, 32.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.991A  pdb=" N   ILE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.789A  pdb=" N   ASP H  90 " --> pdb=" O   LYS H  87 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'L' and resid 81 through 85
      removed outlier: 3.525A  pdb=" N   ASP L  84 " --> pdb=" O   GLN L  81 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER L  85 " --> pdb=" O   SER L  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 81 through 85'
    Processing helix  chain 'R' and resid 349 through 353
      removed outlier: 3.533A  pdb=" N   TRP R 353 " --> pdb=" O   VAL R 350 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 364 through 371
      removed outlier: 3.966A  pdb=" N   VAL R 367 " --> pdb=" O   ASP R 364 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU R 368 " --> pdb=" O   TYR R 365 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   TYR R 369 " --> pdb=" O   SER R 366 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ASN R 370 " --> pdb=" O   VAL R 367 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU R 371 " --> pdb=" O   LEU R 368 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 364 through 371'
    Processing helix  chain 'R' and resid 405 through 407
      No H-bonds generated for 'chain 'R' and resid 405 through 407'
    Processing helix  chain 'R' and resid 417 through 422
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.568A  pdb=" N   GLU A  10 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY A  49 " --> pdb=" O   TRP A  36 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   ARG A  38 " --> pdb=" O   TRP A  47 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   TRP A  47 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.568A  pdb=" N   GLU A  10 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7
      removed outlier: 3.553A  pdb=" N   CYS B  23 " --> pdb=" O   PHE B  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
    Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 48
      removed outlier: 5.559A  pdb=" N   LEU B  46 " --> pdb=" O   GLN B  37 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   GLN B  37 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.239A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.771A  pdb=" N   CYS H  96 " --> pdb=" O   GLY H 111 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.239A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7
      removed outlier: 3.505A  pdb=" N   PHE L  73 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU L  72 " --> pdb=" O   SER L  69 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER L  65 " --> pdb=" O   THR L  76 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.156A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 107 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TYR L  88 " --> pdb=" O   THR L 104 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   LEU L  35 " --> pdb=" O   TYR L  51 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   TYR L  51 " --> pdb=" O   LEU L  35 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 354 through 358
    Processing sheet with id=AB3, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AB4, first strand: chain 'R' and resid 473 through 474

    153 hydrogen bonds defined for protein.
    372 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: 2.16

  Time building geometry restraints manager: 1.58 seconds

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

  Histogram of bond lengths:
        1.21 -     1.35: 1635
        1.35 -     1.48: 1497
        1.48 -     1.62: 2055
        1.62 -     1.76: 0
        1.76 -     1.89: 28
  Bond restraints: 5215
  Sorted by residual:
  bond pdb=" CB  CYS R 432 "
       pdb=" SG  CYS R 432 "
    ideal  model  delta    sigma   weight residual
    1.808  1.890 -0.082 3.30e-02 9.18e+02 6.24e+00
  bond pdb=" CB  LYS H  87 "
       pdb=" CG  LYS H  87 "
    ideal  model  delta    sigma   weight residual
    1.520  1.573 -0.053 3.00e-02 1.11e+03 3.12e+00
  bond pdb=" CG  LYS H  87 "
       pdb=" CD  LYS H  87 "
    ideal  model  delta    sigma   weight residual
    1.520  1.571 -0.051 3.00e-02 1.11e+03 2.85e+00
  bond pdb=" CA  ASP H  54 "
       pdb=" CB  ASP H  54 "
    ideal  model  delta    sigma   weight residual
    1.533  1.561 -0.028 1.66e-02 3.63e+03 2.82e+00
  bond pdb=" CB  GLN A  62 "
       pdb=" CG  GLN A  62 "
    ideal  model  delta    sigma   weight residual
    1.520  1.569 -0.049 3.00e-02 1.11e+03 2.70e+00
  ... (remaining 5210 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.04: 6966
        3.04 -     6.08: 104
        6.08 -     9.12: 15
        9.12 -    12.15: 2
       12.15 -    15.19: 2
  Bond angle restraints: 7089
  Sorted by residual:
  angle pdb=" CA  CYS R 379 "
        pdb=" CB  CYS R 379 "
        pdb=" SG  CYS R 379 "
      ideal   model   delta    sigma   weight residual
     114.40  129.59  -15.19 2.30e+00 1.89e-01 4.36e+01
  angle pdb=" N   CYS R 361 "
        pdb=" CA  CYS R 361 "
        pdb=" C   CYS R 361 "
      ideal   model   delta    sigma   weight residual
     109.18  116.62   -7.44 1.42e+00 4.96e-01 2.74e+01
  angle pdb=" CB  LYS H  87 "
        pdb=" CG  LYS H  87 "
        pdb=" CD  LYS H  87 "
      ideal   model   delta    sigma   weight residual
     111.30  123.07  -11.77 2.30e+00 1.89e-01 2.62e+01
  angle pdb=" N   CYS R 379 "
        pdb=" CA  CYS R 379 "
        pdb=" C   CYS R 379 "
      ideal   model   delta    sigma   weight residual
     108.96  115.12   -6.16 1.49e+00 4.50e-01 1.71e+01
  angle pdb=" C   SER L  32 "
        pdb=" N   THR L  33 "
        pdb=" CA  THR L  33 "
      ideal   model   delta    sigma   weight residual
     122.07  127.98   -5.91 1.43e+00 4.89e-01 1.71e+01
  ... (remaining 7084 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 2761
       17.38 -    34.76: 271
       34.76 -    52.13: 49
       52.13 -    69.51: 8
       69.51 -    86.89: 8
  Dihedral angle restraints: 3097
    sinusoidal: 1227
      harmonic: 1870
  Sorted by residual:
  dihedral pdb=" CB  CYS R 391 "
           pdb=" SG  CYS R 391 "
           pdb=" SG  CYS R 525 "
           pdb=" CB  CYS R 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   14.17   78.83     1      1.00e+01 1.00e-02 7.74e+01
  dihedral pdb=" CA  LEU A  99 "
           pdb=" C   LEU A  99 "
           pdb=" N   PHE A 100 "
           pdb=" CA  PHE A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -141.97  -38.03     0      5.00e+00 4.00e-02 5.78e+01
  dihedral pdb=" CA  CYS R 361 "
           pdb=" C   CYS R 361 "
           pdb=" N   VAL R 362 "
           pdb=" CA  VAL R 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.38   33.62     0      5.00e+00 4.00e-02 4.52e+01
  ... (remaining 3094 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 694
       0.098 -    0.196: 66
       0.196 -    0.294: 9
       0.294 -    0.393: 2
       0.393 -    0.491: 1
  Chirality restraints: 772
  Sorted by residual:
  chirality pdb=" C1  FUC X   3 "
            pdb=" O6  NAG X   1 "
            pdb=" C2  FUC X   3 "
            pdb=" O5  FUC X   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.34   -0.06 2.00e-02 2.50e+03 8.53e+00
  chirality pdb=" CB  ILE H  34 "
            pdb=" CA  ILE H  34 "
            pdb=" CG1 ILE H  34 "
            pdb=" CG2 ILE H  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.15    0.49 2.00e-01 2.50e+01 6.02e+00
  chirality pdb=" CB  ILE H  51 "
            pdb=" CA  ILE H  51 "
            pdb=" CG1 ILE H  51 "
            pdb=" CG2 ILE H  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.32 2.00e-01 2.50e+01 2.55e+00
  ... (remaining 769 not shown)

  Planarity restraints: 915
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG X   1 "    0.107 2.00e-02 2.50e+03   8.85e-02 9.78e+01
        pdb=" C7  NAG X   1 "   -0.028 2.00e-02 2.50e+03
        pdb=" C8  NAG X   1 "    0.081 2.00e-02 2.50e+03
        pdb=" N2  NAG X   1 "   -0.141 2.00e-02 2.50e+03
        pdb=" O7  NAG X   1 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG X   2 "   -0.059 2.00e-02 2.50e+03   4.85e-02 2.94e+01
        pdb=" C7  NAG X   2 "    0.019 2.00e-02 2.50e+03
        pdb=" C8  NAG X   2 "   -0.046 2.00e-02 2.50e+03
        pdb=" N2  NAG X   2 "    0.076 2.00e-02 2.50e+03
        pdb=" O7  NAG X   2 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 107 "   -0.049 5.00e-02 4.00e+02   7.50e-02 9.00e+00
        pdb=" N   PRO A 108 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A 108 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 108 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 912 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1538
        2.82 -     3.34: 3997
        3.34 -     3.86: 8403
        3.86 -     4.38: 9574
        4.38 -     4.90: 17257
  Nonbonded interactions: 40769
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 469 "
            pdb=" OE1 GLU R 471 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   GLY H   8 "
            pdb=" OG1 THR H 114 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" OE2 GLU R 406 "
            pdb=" OH  TYR R 495 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   ASN R 439 "
            pdb=" OG  SER R 443 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   SER A 107 "
            pdb=" OG  SER A 107 "
     model   vdw
     2.359 3.040
  ... (remaining 40764 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 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:             3.970
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.160
  Find NCS groups from input model:        0.070
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082   5224  Z= 0.257
  Angle     :  0.965  15.192   7109  Z= 0.518
  Chirality :  0.062   0.491    772
  Planarity :  0.008   0.088    915
  Dihedral  : 14.239  86.888   1888
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.55 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.49 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.32), residues: 641
  helix: -4.93 (0.34), residues: 22
  sheet: -1.28 (0.32), residues: 284
  loop : -1.57 (0.30), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  36 
 HIS   0.006   0.002   HIS H  35 
 PHE   0.020   0.002   PHE R 347 
 TYR   0.030   0.002   TYR R 380 
 ARG   0.015   0.001   ARG B  18 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00714 (    1)
  link_BETA1-4         : angle       1.78089 (    3)
  hydrogen bonds       : bond        0.26509 (  137)
  hydrogen bonds       : angle      11.59964 (  372)
  link_BETA1-6         : bond        0.00773 (    1)
  link_BETA1-6         : angle       0.98737 (    3)
  SS BOND              : bond        0.01088 (    7)
  SS BOND              : angle       3.29239 (   14)
  covalent geometry    : bond        0.00589 ( 5215)
  covalent geometry    : angle       0.95412 ( 7089)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.514 
Fit side-chains
REVERT: R  378 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7673 (pttm)
REVERT: R  390 LEU cc_start: 0.8148 (tp) cc_final: 0.7756 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1436
  time to fit residues: 20.7917
Evaluate side-chains
  92 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   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   6 GLN
H  62 GLN
H 112 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.124927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.100932 restraints weight = 6737.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 2.01
r_work: 0.2930 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5224  Z= 0.180
  Angle     :  0.636   7.314   7109  Z= 0.340
  Chirality :  0.048   0.238    772
  Planarity :  0.005   0.062    915
  Dihedral  :  5.378  28.883    773
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.54 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.32), residues: 641
  helix: -4.91 (0.37), residues: 22
  sheet: -1.09 (0.31), residues: 288
  loop : -1.39 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP L  96 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.011   0.001   PHE B  73 
 TYR   0.017   0.001   TYR L  93 
 ARG   0.004   0.000   ARG B  90 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00033 (    1)
  link_BETA1-4         : angle       1.54911 (    3)
  hydrogen bonds       : bond        0.05183 (  137)
  hydrogen bonds       : angle       8.09760 (  372)
  link_BETA1-6         : bond        0.00450 (    1)
  link_BETA1-6         : angle       1.62022 (    3)
  SS BOND              : bond        0.00634 (    7)
  SS BOND              : angle       2.13312 (   14)
  covalent geometry    : bond        0.00418 ( 5215)
  covalent geometry    : angle       0.62858 ( 7089)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.517 
Fit side-chains
REVERT: R  390 LEU cc_start: 0.8357 (tp) cc_final: 0.8148 (tp)
  outliers start: 7
  outliers final: 6
  residues processed: 96
  average time/residue: 0.1438
  time to fit residues: 18.4990
Evaluate side-chains
  94 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain R residue  336 CYS
Chi-restraints excluded: chain R residue  349 SER
Chi-restraints excluded: chain R residue  392 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   chunk 55 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.5978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.125081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.101459 restraints weight = 6735.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.98
r_work: 0.2947 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5224  Z= 0.146
  Angle     :  0.576   6.558   7109  Z= 0.306
  Chirality :  0.046   0.185    772
  Planarity :  0.004   0.056    915
  Dihedral  :  4.940  29.870    773
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.75 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.16 %
    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: -1.98 (0.33), residues: 641
  helix: -4.98 (0.29), residues: 28
  sheet: -0.86 (0.31), residues: 288
  loop : -1.31 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L  96 
 HIS   0.003   0.001   HIS H  27 
 PHE   0.010   0.001   PHE R 490 
 TYR   0.014   0.001   TYR L  93 
 ARG   0.006   0.000   ARG L  18 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00001 (    1)
  link_BETA1-4         : angle       1.66890 (    3)
  hydrogen bonds       : bond        0.04123 (  137)
  hydrogen bonds       : angle       7.14673 (  372)
  link_BETA1-6         : bond        0.00329 (    1)
  link_BETA1-6         : angle       1.33798 (    3)
  SS BOND              : bond        0.00391 (    7)
  SS BOND              : angle       2.00287 (   14)
  covalent geometry    : bond        0.00337 ( 5215)
  covalent geometry    : angle       0.56853 ( 7089)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A  110 ASP cc_start: 0.6605 (m-30) cc_final: 0.6346 (m-30)
REVERT: H   87 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7748 (tppt)
REVERT: R  390 LEU cc_start: 0.8357 (tp) cc_final: 0.8145 (tp)
  outliers start: 12
  outliers final: 8
  residues processed: 101
  average time/residue: 0.1450
  time to fit residues: 19.8982
Evaluate side-chains
  96 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ASN
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain R residue  336 CYS
Chi-restraints excluded: chain R residue  349 SER
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  392 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0570
   chunk 40 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
R 487 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.124827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.101189 restraints weight = 6866.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 1.99
r_work: 0.2940 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5224  Z= 0.145
  Angle     :  0.563   6.291   7109  Z= 0.298
  Chirality :  0.046   0.193    772
  Planarity :  0.004   0.054    915
  Dihedral  :  4.773  28.267    773
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.40 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.16 %
    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: -1.88 (0.33), residues: 641
  helix: -4.97 (0.28), residues: 28
  sheet: -0.76 (0.31), residues: 289
  loop : -1.27 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP L  96 
 HIS   0.003   0.001   HIS H  27 
 PHE   0.009   0.001   PHE A 100 
 TYR   0.014   0.001   TYR L  93 
 ARG   0.004   0.000   ARG L  18 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00010 (    1)
  link_BETA1-4         : angle       1.63597 (    3)
  hydrogen bonds       : bond        0.03888 (  137)
  hydrogen bonds       : angle       6.75639 (  372)
  link_BETA1-6         : bond        0.00256 (    1)
  link_BETA1-6         : angle       1.35823 (    3)
  SS BOND              : bond        0.00574 (    7)
  SS BOND              : angle       2.01376 (   14)
  covalent geometry    : bond        0.00335 ( 5215)
  covalent geometry    : angle       0.55451 ( 7089)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.609 
Fit side-chains
REVERT: A  110 ASP cc_start: 0.6701 (m-30) cc_final: 0.6404 (m-30)
  outliers start: 15
  outliers final: 10
  residues processed: 104
  average time/residue: 0.1588
  time to fit residues: 21.9189
Evaluate side-chains
  103 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ASN
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   10 SER
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain R residue  336 CYS
Chi-restraints excluded: chain R residue  349 SER
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  392 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 47 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.123548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.099609 restraints weight = 6846.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.02
r_work: 0.2925 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5224  Z= 0.174
  Angle     :  0.579   6.481   7109  Z= 0.305
  Chirality :  0.046   0.189    772
  Planarity :  0.004   0.054    915
  Dihedral  :  4.775  28.822    773
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 18.50 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.16 %
    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: -1.87 (0.33), residues: 641
  helix: -5.01 (0.24), residues: 28
  sheet: -0.77 (0.31), residues: 292
  loop : -1.25 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP L  96 
 HIS   0.003   0.001   HIS H  27 
 PHE   0.010   0.001   PHE A  95 
 TYR   0.016   0.001   TYR L  93 
 ARG   0.006   0.000   ARG L  18 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00107 (    1)
  link_BETA1-4         : angle       1.72570 (    3)
  hydrogen bonds       : bond        0.03847 (  137)
  hydrogen bonds       : angle       6.48532 (  372)
  link_BETA1-6         : bond        0.00262 (    1)
  link_BETA1-6         : angle       1.43539 (    3)
  SS BOND              : bond        0.00385 (    7)
  SS BOND              : angle       1.96032 (   14)
  covalent geometry    : bond        0.00408 ( 5215)
  covalent geometry    : angle       0.57103 ( 7089)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A  110 ASP cc_start: 0.6713 (m-30) cc_final: 0.6487 (m-30)
REVERT: H   10 GLU cc_start: 0.8467 (mp0) cc_final: 0.8191 (mp0)
REVERT: H   87 LYS cc_start: 0.7943 (mmmt) cc_final: 0.7540 (tppt)
  outliers start: 16
  outliers final: 12
  residues processed: 101
  average time/residue: 0.1547
  time to fit residues: 20.8338
Evaluate side-chains
  104 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ASN
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   10 SER
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain R residue  336 CYS
Chi-restraints excluded: chain R residue  349 SER
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  392 PHE
Chi-restraints excluded: chain R residue  468 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.4186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.119454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.095239 restraints weight = 6924.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 2.02
r_work: 0.2856 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   5224  Z= 0.273
  Angle     :  0.658   7.090   7109  Z= 0.346
  Chirality :  0.049   0.229    772
  Planarity :  0.005   0.059    915
  Dihedral  :  5.132  29.488    773
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.86 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.33), residues: 641
  helix: -4.83 (0.35), residues: 29
  sheet: -0.93 (0.31), residues: 293
  loop : -1.42 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H  50 
 HIS   0.005   0.002   HIS H  35 
 PHE   0.012   0.002   PHE A 100 
 TYR   0.021   0.002   TYR L  93 
 ARG   0.008   0.001   ARG L  18 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00365 (    1)
  link_BETA1-4         : angle       2.01757 (    3)
  hydrogen bonds       : bond        0.04319 (  137)
  hydrogen bonds       : angle       6.59922 (  372)
  link_BETA1-6         : bond        0.00002 (    1)
  link_BETA1-6         : angle       1.60622 (    3)
  SS BOND              : bond        0.00576 (    7)
  SS BOND              : angle       2.40137 (   14)
  covalent geometry    : bond        0.00641 ( 5215)
  covalent geometry    : angle       0.64763 ( 7089)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.553 
Fit side-chains
REVERT: A  110 ASP cc_start: 0.6967 (m-30) cc_final: 0.6750 (m-30)
  outliers start: 17
  outliers final: 14
  residues processed: 98
  average time/residue: 0.1439
  time to fit residues: 19.0345
Evaluate side-chains
  101 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ASN
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   10 SER
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain R residue  336 CYS
Chi-restraints excluded: chain R residue  349 SER
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  392 PHE
Chi-restraints excluded: chain R residue  468 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0470
   chunk 26 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
H  43 GLN
** L  95 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 = 0.3358 r_free = 0.3358 target = 0.123043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.098984 restraints weight = 6769.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 2.01
r_work: 0.2910 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5224  Z= 0.146
  Angle     :  0.577   6.565   7109  Z= 0.303
  Chirality :  0.046   0.189    772
  Planarity :  0.004   0.053    915
  Dihedral  :  4.846  29.482    773
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.32 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.16 %
    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: -1.89 (0.33), residues: 641
  helix: -4.77 (0.41), residues: 23
  sheet: -0.82 (0.31), residues: 291
  loop : -1.31 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L  96 
 HIS   0.003   0.001   HIS H  27 
 PHE   0.011   0.001   PHE A 100 
 TYR   0.015   0.001   TYR L  93 
 ARG   0.007   0.000   ARG L  18 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00003 (    1)
  link_BETA1-4         : angle       1.95696 (    3)
  hydrogen bonds       : bond        0.03655 (  137)
  hydrogen bonds       : angle       6.42368 (  372)
  link_BETA1-6         : bond        0.00276 (    1)
  link_BETA1-6         : angle       1.27877 (    3)
  SS BOND              : bond        0.00528 (    7)
  SS BOND              : angle       2.05068 (   14)
  covalent geometry    : bond        0.00343 ( 5215)
  covalent geometry    : angle       0.56858 ( 7089)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.489 
Fit side-chains
REVERT: H   10 GLU cc_start: 0.8510 (mp0) cc_final: 0.7599 (mp0)
REVERT: H  112 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8644 (pt0)
  outliers start: 18
  outliers final: 15
  residues processed: 99
  average time/residue: 0.1431
  time to fit residues: 19.0547
Evaluate side-chains
  103 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ASN
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   10 SER
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   44 GLN
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain R residue  336 CYS
Chi-restraints excluded: chain R residue  349 SER
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  391 CYS
Chi-restraints excluded: chain R residue  392 PHE
Chi-restraints excluded: chain R residue  468 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0470
   chunk 26 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 32 optimal weight:    0.2980
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
H  43 GLN
** L  95 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 = 0.3380 r_free = 0.3380 target = 0.124547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.100304 restraints weight = 6759.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 2.02
r_work: 0.2928 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5224  Z= 0.143
  Angle     :  0.569   6.434   7109  Z= 0.300
  Chirality :  0.046   0.219    772
  Planarity :  0.004   0.054    915
  Dihedral  :  4.690  27.894    773
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 19.78 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.16 %
    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: -1.78 (0.33), residues: 641
  helix: -4.83 (0.41), residues: 22
  sheet: -0.73 (0.31), residues: 290
  loop : -1.27 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  96 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.010   0.001   PHE A 100 
 TYR   0.014   0.001   TYR L  93 
 ARG   0.007   0.000   ARG L  18 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00052 (    1)
  link_BETA1-4         : angle       1.80379 (    3)
  hydrogen bonds       : bond        0.03605 (  137)
  hydrogen bonds       : angle       6.29554 (  372)
  link_BETA1-6         : bond        0.00212 (    1)
  link_BETA1-6         : angle       1.30716 (    3)
  SS BOND              : bond        0.00584 (    7)
  SS BOND              : angle       1.96907 (   14)
  covalent geometry    : bond        0.00335 ( 5215)
  covalent geometry    : angle       0.56111 ( 7089)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A  110 ASP cc_start: 0.6652 (m-30) cc_final: 0.6346 (m-30)
REVERT: H  112 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8608 (pt0)
  outliers start: 19
  outliers final: 13
  residues processed: 96
  average time/residue: 0.1359
  time to fit residues: 17.5966
Evaluate side-chains
  99 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ASN
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   10 SER
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   32 SER
Chi-restraints excluded: chain R residue  336 CYS
Chi-restraints excluded: chain R residue  349 SER
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  391 CYS
Chi-restraints excluded: chain R residue  392 PHE
Chi-restraints excluded: chain R residue  468 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B  24 GLN
H  43 GLN
** L  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 370 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.122233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.098581 restraints weight = 6822.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 1.97
r_work: 0.2905 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5224  Z= 0.201
  Angle     :  0.608   7.448   7109  Z= 0.324
  Chirality :  0.047   0.224    772
  Planarity :  0.004   0.054    915
  Dihedral  :  4.828  28.381    773
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 19.60 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.16 %
    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: -1.77 (0.33), residues: 641
  helix: -4.72 (0.47), residues: 23
  sheet: -0.71 (0.31), residues: 291
  loop : -1.26 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L  96 
 HIS   0.003   0.001   HIS H  27 
 PHE   0.011   0.001   PHE A  95 
 TYR   0.018   0.002   TYR L  93 
 ARG   0.008   0.000   ARG L  18 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00125 (    1)
  link_BETA1-4         : angle       1.86362 (    3)
  hydrogen bonds       : bond        0.03748 (  137)
  hydrogen bonds       : angle       6.27960 (  372)
  link_BETA1-6         : bond        0.00109 (    1)
  link_BETA1-6         : angle       1.44573 (    3)
  SS BOND              : bond        0.00603 (    7)
  SS BOND              : angle       2.06882 (   14)
  covalent geometry    : bond        0.00474 ( 5215)
  covalent geometry    : angle       0.59995 ( 7089)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A  110 ASP cc_start: 0.6645 (m-30) cc_final: 0.6327 (m-30)
REVERT: H  112 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8675 (pt0)
  outliers start: 22
  outliers final: 17
  residues processed: 95
  average time/residue: 0.1417
  time to fit residues: 18.3203
Evaluate side-chains
  102 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ASN
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   10 SER
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   32 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain R residue  336 CYS
Chi-restraints excluded: chain R residue  349 SER
Chi-restraints excluded: chain R residue  370 ASN
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  391 CYS
Chi-restraints excluded: chain R residue  392 PHE
Chi-restraints excluded: chain R residue  468 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 41 optimal weight:    0.4980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  24 GLN
H  43 GLN
** L  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.123611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.099786 restraints weight = 6765.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 1.99
r_work: 0.2925 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5224  Z= 0.156
  Angle     :  0.590   7.445   7109  Z= 0.313
  Chirality :  0.047   0.208    772
  Planarity :  0.004   0.053    915
  Dihedral  :  4.772  28.296    773
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 20.33 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.16 %
    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: -1.72 (0.33), residues: 641
  helix: -4.74 (0.45), residues: 23
  sheet: -0.66 (0.31), residues: 290
  loop : -1.24 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  96 
 HIS   0.003   0.001   HIS H  27 
 PHE   0.011   0.001   PHE A 100 
 TYR   0.015   0.001   TYR L  93 
 ARG   0.007   0.000   ARG L  18 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00003 (    1)
  link_BETA1-4         : angle       1.85049 (    3)
  hydrogen bonds       : bond        0.03618 (  137)
  hydrogen bonds       : angle       6.25090 (  372)
  link_BETA1-6         : bond        0.00258 (    1)
  link_BETA1-6         : angle       1.29965 (    3)
  SS BOND              : bond        0.00596 (    7)
  SS BOND              : angle       1.95834 (   14)
  covalent geometry    : bond        0.00367 ( 5215)
  covalent geometry    : angle       0.58224 ( 7089)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.543 
Fit side-chains
REVERT: A  110 ASP cc_start: 0.6601 (m-30) cc_final: 0.6313 (m-30)
REVERT: H  112 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8631 (pt0)
  outliers start: 19
  outliers final: 17
  residues processed: 93
  average time/residue: 0.1424
  time to fit residues: 18.0162
Evaluate side-chains
  99 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ASN
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   10 SER
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue   99 GLU
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   32 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain R residue  336 CYS
Chi-restraints excluded: chain R residue  349 SER
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain R residue  391 CYS
Chi-restraints excluded: chain R residue  392 PHE
Chi-restraints excluded: chain R residue  468 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
H  43 GLN
** L  95 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 = 0.3355 r_free = 0.3355 target = 0.122551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.098562 restraints weight = 6896.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.01
r_work: 0.2904 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5224  Z= 0.187
  Angle     :  0.599   7.741   7109  Z= 0.314
  Chirality :  0.047   0.218    772
  Planarity :  0.004   0.054    915
  Dihedral  :  4.789  28.147    773
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.15 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.16 %
    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: -1.72 (0.33), residues: 641
  helix: -4.70 (0.49), residues: 23
  sheet: -0.67 (0.31), residues: 291
  loop : -1.24 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L  96 
 HIS   0.003   0.001   HIS H  27 
 PHE   0.010   0.001   PHE A 100 
 TYR   0.017   0.002   TYR L  93 
 ARG   0.007   0.000   ARG L  18 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00020 (    1)
  link_BETA1-4         : angle       1.93209 (    3)
  hydrogen bonds       : bond        0.03658 (  137)
  hydrogen bonds       : angle       6.23548 (  372)
  link_BETA1-6         : bond        0.00170 (    1)
  link_BETA1-6         : angle       1.37566 (    3)
  SS BOND              : bond        0.00628 (    7)
  SS BOND              : angle       2.04061 (   14)
  covalent geometry    : bond        0.00442 ( 5215)
  covalent geometry    : angle       0.59077 ( 7089)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3366.43 seconds
wall clock time: 58 minutes 52.73 seconds (3532.73 seconds total)