Starting phenix.real_space_refine
on Wed Jul 23 20:21:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y0o_33551/07_2025/7y0o_33551.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y0o_33551/07_2025/7y0o_33551.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y0o_33551/07_2025/7y0o_33551.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y0o_33551/07_2025/7y0o_33551.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y0o_33551/07_2025/7y0o_33551.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y0o_33551/07_2025/7y0o_33551.cif"
  }
  resolution = 4.4
  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=   0.042 sd=   1.426
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      19      5.16       5
     C    2644      2.51       5
     N     701      2.21       5
     O     821      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4185
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1513
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 22
    Chain: "H"
      Number of atoms: 889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 889
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
    Chain: "L"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 818
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 947
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 5, 'TRANS': 117}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 17
          Classifications: {'water': 17}
          Link IDs: {None: 16}
  Time building chain proxies: 3.46, per 1000 atoms: 0.83
  Number of scatterers: 4185
  At special positions: 0
  Unit cell: (85.6, 87.74, 111.28, 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      19     16.00
     O     821      8.00
     N     701      7.00
     C    2644      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " 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
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 472.6 milliseconds
  

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  980

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 11 sheets defined
      7.4% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 3.521A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 5.878A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 410 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
      removed outlier: 3.824A  pdb=" N   ASN A 422 " --> pdb=" O   ILE A 418 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 61 through 65
      removed outlier: 3.673A  pdb=" N   GLN H  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
      removed outlier: 4.393A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASP A 398 " --> pdb=" O   VAL A 512 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A 512 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   TYR A 508 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'H' and resid 16 through 17
      removed outlier: 3.942A  pdb=" N   ALA H  16 " --> pdb=" O   SER H  85 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER H  85 " --> pdb=" O   ALA H  16 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 23
      removed outlier: 3.827A  pdb=" N   GLU H  82 " --> pdb=" O   THR H  69 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 51
      removed outlier: 4.998A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER H  35 " --> pdb=" O   ALA H  96 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.617A  pdb=" N   ALA L  13 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR L 102 " --> pdb=" O   TYR L  86 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.398A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR L  49 " --> pdb=" O   SER L  53 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 62 through 67
      removed outlier: 3.623A  pdb=" N   SER L  65 " --> pdb=" O   THR L  72 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   THR L  72 " --> pdb=" O   SER L  65 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER L  67 " --> pdb=" O   ASP L  70 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 6 through 7
      removed outlier: 3.904A  pdb=" N   CYS B  22 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL B  79 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 11 through 12
    Processing sheet with id=AB2, first strand: chain 'B' and resid 58 through 60
      removed outlier: 3.666A  pdb=" N   ARG B  59 " --> pdb=" O   ASP B  50 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   ALA B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   ALA B  40 " --> pdb=" O   ALA B  44 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)

    77 hydrogen bonds defined for protein.
    171 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.94

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1337
        1.35 -     1.47: 1148
        1.47 -     1.59: 1764
        1.59 -     1.71: 0
        1.71 -     1.83: 24
  Bond restraints: 4273
  Sorted by residual:
  bond pdb=" CB  GLN L  38 "
       pdb=" CG  GLN L  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.31e+00
  bond pdb=" C   SER A 477 "
       pdb=" N   THR A 478 "
    ideal  model  delta    sigma   weight residual
    1.331  1.311  0.021 1.63e-02 3.76e+03 1.61e+00
  bond pdb=" CA  VAL A 483 "
       pdb=" CB  VAL A 483 "
    ideal  model  delta    sigma   weight residual
    1.547  1.568 -0.021 1.68e-02 3.54e+03 1.56e+00
  bond pdb=" CG  GLN L  38 "
       pdb=" CD  GLN L  38 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.47e+00
  bond pdb=" C   GLY H  26 "
       pdb=" N   TYR H  27 "
    ideal  model  delta    sigma   weight residual
    1.325  1.339 -0.014 1.14e-02 7.69e+03 1.47e+00
  ... (remaining 4268 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 5635
        2.55 -     5.10: 150
        5.10 -     7.66: 16
        7.66 -    10.21: 2
       10.21 -    12.76: 2
  Bond angle restraints: 5805
  Sorted by residual:
  angle pdb=" C   TYR H  27 "
        pdb=" CA  TYR H  27 "
        pdb=" CB  TYR H  27 "
      ideal   model   delta    sigma   weight residual
     115.79  109.40    6.39 1.19e+00 7.06e-01 2.88e+01
  angle pdb=" CB  GLN L  38 "
        pdb=" CG  GLN L  38 "
        pdb=" CD  GLN L  38 "
      ideal   model   delta    sigma   weight residual
     112.60  118.45   -5.85 1.70e+00 3.46e-01 1.19e+01
  angle pdb=" CA  LEU B 119 "
        pdb=" CB  LEU B 119 "
        pdb=" CG  LEU B 119 "
      ideal   model   delta    sigma   weight residual
     116.30  127.53  -11.23 3.50e+00 8.16e-02 1.03e+01
  angle pdb=" C   ALA L  50 "
        pdb=" N   ALA L  51 "
        pdb=" CA  ALA L  51 "
      ideal   model   delta    sigma   weight residual
     121.54  127.42   -5.88 1.91e+00 2.74e-01 9.49e+00
  angle pdb=" C   ASN A 354 "
        pdb=" N   ARG A 355 "
        pdb=" CA  ARG A 355 "
      ideal   model   delta    sigma   weight residual
     122.59  127.38   -4.79 1.57e+00 4.06e-01 9.30e+00
  ... (remaining 5800 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 2189
       16.92 -    33.83: 248
       33.83 -    50.75: 55
       50.75 -    67.66: 8
       67.66 -    84.57: 8
  Dihedral angle restraints: 2508
    sinusoidal: 954
      harmonic: 1554
  Sorted by residual:
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   11.68   81.32     1      1.00e+01 1.00e-02 8.15e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.12  -68.12     1      1.00e+01 1.00e-02 6.02e+01
  dihedral pdb=" CA  ASN A 481 "
           pdb=" C   ASN A 481 "
           pdb=" N   GLY A 482 "
           pdb=" CA  GLY A 482 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.38  -28.62     0      5.00e+00 4.00e-02 3.28e+01
  ... (remaining 2505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 539
       0.085 -    0.170: 72
       0.170 -    0.254: 2
       0.254 -    0.339: 2
       0.339 -    0.424: 1
  Chirality restraints: 616
  Sorted by residual:
  chirality pdb=" CB  ILE A 410 "
            pdb=" CA  ILE A 410 "
            pdb=" CG1 ILE A 410 "
            pdb=" CG2 ILE A 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.22    0.42 2.00e-01 2.50e+01 4.49e+00
  chirality pdb=" CB  ILE H  52 "
            pdb=" CA  ILE H  52 "
            pdb=" CG1 ILE H  52 "
            pdb=" CG2 ILE H  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CB  VAL B  98 "
            pdb=" CA  VAL B  98 "
            pdb=" CG1 VAL B  98 "
            pdb=" CG2 VAL B  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.94e+00
  ... (remaining 613 not shown)

  Planarity restraints: 755
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  36 "   -0.018 2.00e-02 2.50e+03   1.98e-02 9.80e+00
        pdb=" CG  TRP B  36 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  36 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  36 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  36 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  36 "    0.013 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  36 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  36 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  36 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 425 "    0.044 5.00e-02 4.00e+02   6.74e-02 7.26e+00
        pdb=" N   PRO A 426 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 426 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 426 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 353 "    0.014 2.00e-02 2.50e+03   1.70e-02 7.20e+00
        pdb=" CG  TRP A 353 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 353 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 353 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 353 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 353 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 353 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 353 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 353 "    0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 353 "    0.001 2.00e-02 2.50e+03
  ... (remaining 752 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 911
        2.78 -     3.31: 3769
        3.31 -     3.84: 7051
        3.84 -     4.37: 7661
        4.37 -     4.90: 12927
  Nonbonded interactions: 32319
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 111 "
            pdb=" O   HOH B 201 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   LYS H  12 "
            pdb=" OG  SER H  87 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OG  SER B 123 "
            pdb=" O   HOH B 202 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OG1 THR B 118 "
            pdb=" O   HOH B 203 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   VAL A 367 "
            pdb=" OG  SER A 371 "
     model   vdw
     2.309 3.040
  ... (remaining 32314 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:             4.580
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.930
  Find NCS groups from input model:        0.040
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5619
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      :  0.004   0.046   4280  Z= 0.193
  Angle     :  0.931  12.762   5819  Z= 0.481
  Chirality :  0.058   0.424    616
  Planarity :  0.006   0.067    755
  Dihedral  : 15.066  84.574   1507
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.76 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.24 (0.32), residues: 533
  helix: -4.20 (0.65), residues: 30
  sheet: -1.83 (0.42), residues: 144
  loop : -2.21 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.004   TRP B  36 
 HIS   0.006   0.004   HIS A 519 
 PHE   0.014   0.002   PHE B  27 
 TYR   0.022   0.002   TYR B  95 
 ARG   0.011   0.001   ARG A 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.31887 (   77)
  hydrogen bonds       : angle      11.64770 (  171)
  SS BOND              : bond        0.00925 (    7)
  SS BOND              : angle       1.97770 (   14)
  covalent geometry    : bond        0.00411 ( 4273)
  covalent geometry    : angle       0.92746 ( 5805)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.485 
Fit side-chains
REVERT: A  353 TRP cc_start: 0.4437 (p-90) cc_final: 0.4105 (p-90)
REVERT: H   48 MET cc_start: 0.6276 (mpp) cc_final: 0.5899 (mpp)
REVERT: B   83 MET cc_start: 0.7793 (mpp) cc_final: 0.7583 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1552
  time to fit residues: 11.7268
Evaluate side-chains
  43 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 440 ASN
A 481 ASN
** L   3 GLN ** 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 = 0.3477 r_free = 0.3477 target = 0.050198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.041164 restraints weight = 37893.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.042336 restraints weight = 25684.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.043071 restraints weight = 19050.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5751
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4280  Z= 0.158
  Angle     :  0.713  11.409   5819  Z= 0.370
  Chirality :  0.046   0.159    616
  Planarity :  0.006   0.061    755
  Dihedral  :  6.388  28.997    599
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.94 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  8.37 %
    Favored  : 91.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.42 (0.32), residues: 533
  helix: -3.50 (0.90), residues: 25
  sheet: -2.22 (0.38), residues: 159
  loop : -2.29 (0.29), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.003   TRP H  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.028   0.002   PHE L  98 
 TYR   0.023   0.002   TYR A 449 
 ARG   0.007   0.001   ARG H  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04896 (   77)
  hydrogen bonds       : angle       9.08490 (  171)
  SS BOND              : bond        0.00716 (    7)
  SS BOND              : angle       1.71112 (   14)
  covalent geometry    : bond        0.00355 ( 4273)
  covalent geometry    : angle       0.70926 ( 5805)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.495 
Fit side-chains
REVERT: A  353 TRP cc_start: 0.4873 (p-90) cc_final: 0.4401 (p-90)
REVERT: H   48 MET cc_start: 0.6717 (mpp) cc_final: 0.6305 (mpp)
REVERT: L   38 GLN cc_start: 0.6636 (tp40) cc_final: 0.5998 (pt0)
REVERT: L   98 PHE cc_start: 0.4763 (m-10) cc_final: 0.4322 (m-80)
REVERT: B   34 MET cc_start: 0.6557 (mpp) cc_final: 0.5561 (tmm)
REVERT: B   36 TRP cc_start: 0.5708 (m100) cc_final: 0.5467 (m100)
REVERT: B   46 GLU cc_start: 0.6022 (tm-30) cc_final: 0.5644 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1720
  time to fit residues: 11.7583
Evaluate side-chains
  36 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 ASN
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 116 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.049771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.040644 restraints weight = 37388.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.041836 restraints weight = 25267.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.042705 restraints weight = 18576.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5783
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4280  Z= 0.195
  Angle     :  0.796  13.647   5819  Z= 0.412
  Chirality :  0.049   0.188    616
  Planarity :  0.006   0.061    755
  Dihedral  :  6.969  30.483    599
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 11.82 %
    Favored  : 87.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.53 (0.31), residues: 533
  helix: -2.95 (1.17), residues: 18
  sheet: -2.05 (0.40), residues: 136
  loop : -2.60 (0.27), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP B  47 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.026   0.003   PHE B 105 
 TYR   0.047   0.003   TYR A 449 
 ARG   0.008   0.001   ARG H  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04898 (   77)
  hydrogen bonds       : angle       8.86273 (  171)
  SS BOND              : bond        0.00890 (    7)
  SS BOND              : angle       2.30857 (   14)
  covalent geometry    : bond        0.00432 ( 4273)
  covalent geometry    : angle       0.78926 ( 5805)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7591 (p90) cc_final: 0.7194 (p90)
REVERT: A  391 CYS cc_start: 0.2303 (p) cc_final: 0.2025 (p)
REVERT: H   47 TRP cc_start: 0.5480 (t60) cc_final: 0.5125 (t60)
REVERT: H   48 MET cc_start: 0.6695 (mpp) cc_final: 0.6457 (mpp)
REVERT: B   36 TRP cc_start: 0.5656 (m100) cc_final: 0.5366 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1599
  time to fit residues: 10.7231
Evaluate side-chains
  38 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0970
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
** L   3 GLN ** 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 = 0.3476 r_free = 0.3476 target = 0.049995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.040847 restraints weight = 36410.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.042050 restraints weight = 24528.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.042930 restraints weight = 18037.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5746
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4280  Z= 0.119
  Angle     :  0.664   9.137   5819  Z= 0.343
  Chirality :  0.046   0.161    616
  Planarity :  0.005   0.056    755
  Dihedral  :  6.060  27.874    599
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.69 %
    Favored  : 89.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.25 (0.32), residues: 533
  helix: -2.74 (1.18), residues: 18
  sheet: -1.81 (0.42), residues: 129
  loop : -2.43 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.012   0.002   PHE B 105 
 TYR   0.023   0.002   TYR A 449 
 ARG   0.003   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03736 (   77)
  hydrogen bonds       : angle       8.19421 (  171)
  SS BOND              : bond        0.00556 (    7)
  SS BOND              : angle       1.62586 (   14)
  covalent geometry    : bond        0.00277 ( 4273)
  covalent geometry    : angle       0.65952 ( 5805)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.7718 (p90) cc_final: 0.7248 (p90)
REVERT: H   47 TRP cc_start: 0.5651 (t60) cc_final: 0.5328 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1981
  time to fit residues: 13.3947
Evaluate side-chains
  41 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 47 optimal weight:    0.2980
   chunk 10 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0570
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   3 GLN ** 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 = 0.3475 r_free = 0.3475 target = 0.049982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.040898 restraints weight = 37877.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.042090 restraints weight = 25338.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.043005 restraints weight = 18587.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5738
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4280  Z= 0.119
  Angle     :  0.658   8.979   5819  Z= 0.341
  Chirality :  0.045   0.168    616
  Planarity :  0.005   0.053    755
  Dihedral  :  5.945  27.360    599
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 11.26 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.29 (0.32), residues: 533
  helix: -3.30 (0.94), residues: 24
  sheet: -2.00 (0.39), residues: 141
  loop : -2.31 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 353 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.014   0.002   PHE B 105 
 TYR   0.024   0.002   TYR A 449 
 ARG   0.003   0.000   ARG H  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (   77)
  hydrogen bonds       : angle       7.95924 (  171)
  SS BOND              : bond        0.00651 (    7)
  SS BOND              : angle       1.79000 (   14)
  covalent geometry    : bond        0.00273 ( 4273)
  covalent geometry    : angle       0.65282 ( 5805)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7662 (p90) cc_final: 0.7181 (p90)
REVERT: H   47 TRP cc_start: 0.5528 (t60) cc_final: 0.5235 (t60)
REVERT: H   48 MET cc_start: 0.6609 (mpp) cc_final: 0.6407 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.2439
  time to fit residues: 16.6133
Evaluate side-chains
  39 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0570
   chunk 14 optimal weight:    0.0980
   chunk 31 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
** L   3 GLN ** 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 = 0.3477 r_free = 0.3477 target = 0.050003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.040977 restraints weight = 37144.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.042171 restraints weight = 24860.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.043070 restraints weight = 18275.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5743
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4280  Z= 0.118
  Angle     :  0.656   8.590   5819  Z= 0.341
  Chirality :  0.046   0.175    616
  Planarity :  0.005   0.052    755
  Dihedral  :  5.873  27.522    599
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.32 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.19 (0.33), residues: 533
  helix: -2.60 (1.20), residues: 18
  sheet: -1.92 (0.41), residues: 135
  loop : -2.31 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  36 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.013   0.002   PHE B 105 
 TYR   0.021   0.002   TYR A 449 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (   77)
  hydrogen bonds       : angle       7.81531 (  171)
  SS BOND              : bond        0.00627 (    7)
  SS BOND              : angle       1.72090 (   14)
  covalent geometry    : bond        0.00270 ( 4273)
  covalent geometry    : angle       0.65160 ( 5805)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.520 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7667 (p90) cc_final: 0.7138 (p90)
REVERT: H   47 TRP cc_start: 0.5531 (t60) cc_final: 0.5200 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.2313
  time to fit residues: 16.0147
Evaluate side-chains
  42 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 4 optimal weight:    0.1980
   chunk 25 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    0.1980
   chunk 6 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
** L   3 GLN ** 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 = 0.3487 r_free = 0.3487 target = 0.050379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.041067 restraints weight = 37506.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.042276 restraints weight = 24966.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.043216 restraints weight = 18284.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5745
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4280  Z= 0.120
  Angle     :  0.664   8.407   5819  Z= 0.343
  Chirality :  0.046   0.174    616
  Planarity :  0.005   0.051    755
  Dihedral  :  5.881  26.168    599
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.07 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.21 (0.33), residues: 533
  helix: -3.31 (0.94), residues: 24
  sheet: -1.81 (0.41), residues: 136
  loop : -2.31 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.015   0.002   PHE B 105 
 TYR   0.033   0.002   TYR A 449 
 ARG   0.003   0.000   ARG H  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03336 (   77)
  hydrogen bonds       : angle       7.74971 (  171)
  SS BOND              : bond        0.00527 (    7)
  SS BOND              : angle       1.98319 (   14)
  covalent geometry    : bond        0.00274 ( 4273)
  covalent geometry    : angle       0.65763 ( 5805)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7695 (p90) cc_final: 0.7121 (p90)
REVERT: H   47 TRP cc_start: 0.5522 (t60) cc_final: 0.5225 (t60)
REVERT: B   36 TRP cc_start: 0.5784 (m100) cc_final: 0.5546 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1783
  time to fit residues: 12.1189
Evaluate side-chains
  42 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0170
   chunk 32 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
A 448 ASN
A 481 ASN
** L   3 GLN ** 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 = 0.3484 r_free = 0.3484 target = 0.050094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.041035 restraints weight = 37036.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.042226 restraints weight = 24803.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.043108 restraints weight = 18184.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5747
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4280  Z= 0.133
  Angle     :  0.686  10.399   5819  Z= 0.352
  Chirality :  0.046   0.178    616
  Planarity :  0.005   0.051    755
  Dihedral  :  5.998  26.726    599
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.30 (0.32), residues: 533
  helix: -2.73 (1.18), residues: 18
  sheet: -1.98 (0.40), residues: 141
  loop : -2.39 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 353 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.014   0.002   PHE B 105 
 TYR   0.034   0.002   TYR A 449 
 ARG   0.004   0.001   ARG H  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03470 (   77)
  hydrogen bonds       : angle       7.79631 (  171)
  SS BOND              : bond        0.00618 (    7)
  SS BOND              : angle       1.98875 (   14)
  covalent geometry    : bond        0.00305 ( 4273)
  covalent geometry    : angle       0.67947 ( 5805)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.478 
Fit side-chains
REVERT: H    2 MET cc_start: 0.5128 (ppp) cc_final: 0.4911 (ppp)
REVERT: H    3 GLN cc_start: 0.6409 (pp30) cc_final: 0.6168 (pp30)
REVERT: H   47 TRP cc_start: 0.5467 (t60) cc_final: 0.5189 (t60)
REVERT: B   36 TRP cc_start: 0.5857 (m100) cc_final: 0.5646 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1908
  time to fit residues: 13.8059
Evaluate side-chains
  43 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 48 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 51 optimal weight:    0.1980
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0670
   chunk 2 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0770
   chunk 18 optimal weight:    0.0970
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.1674

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

Flipped N/Q/H residues before XYZ refinement:
A 439 ASN
A 481 ASN
** L   3 GLN ** 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 = 0.3501 r_free = 0.3501 target = 0.050731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.041563 restraints weight = 36735.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.042780 restraints weight = 24885.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.043679 restraints weight = 18405.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5725
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   4280  Z= 0.096
  Angle     :  0.619   5.796   5819  Z= 0.321
  Chirality :  0.046   0.208    616
  Planarity :  0.004   0.049    755
  Dihedral  :  5.348  25.218    599
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.11 (0.33), residues: 533
  helix: -3.33 (0.85), residues: 25
  sheet: -1.92 (0.41), residues: 138
  loop : -2.14 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 353 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.014   0.001   PHE A 400 
 TYR   0.022   0.001   TYR A 449 
 ARG   0.003   0.000   ARG B  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03038 (   77)
  hydrogen bonds       : angle       7.35978 (  171)
  SS BOND              : bond        0.00476 (    7)
  SS BOND              : angle       1.64270 (   14)
  covalent geometry    : bond        0.00218 ( 4273)
  covalent geometry    : angle       0.61461 ( 5805)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7514 (p90) cc_final: 0.6765 (p90)
REVERT: A  457 ARG cc_start: 0.4247 (ttt180) cc_final: 0.3997 (ttp-170)
REVERT: A  458 LYS cc_start: 0.5769 (mmtm) cc_final: 0.5536 (mmtm)
REVERT: H   47 TRP cc_start: 0.5514 (t60) cc_final: 0.5250 (t60)
REVERT: B   85 ARG cc_start: 0.7875 (tpm170) cc_final: 0.7629 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1717
  time to fit residues: 13.4392
Evaluate side-chains
  45 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0070
   chunk 33 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0060
   overall best weight:    0.7818

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
** L   3 GLN ** 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 = 0.3478 r_free = 0.3478 target = 0.049947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.040983 restraints weight = 37978.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.042126 restraints weight = 25923.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.042986 restraints weight = 19352.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5739
moved from start:          0.2683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4280  Z= 0.153
  Angle     :  0.740   9.627   5819  Z= 0.380
  Chirality :  0.049   0.261    616
  Planarity :  0.005   0.051    755
  Dihedral  :  6.227  31.418    599
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.27 (0.32), residues: 533
  helix: -2.77 (1.17), residues: 18
  sheet: -2.01 (0.39), residues: 142
  loop : -2.34 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  36 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.023   0.002   PHE B 105 
 TYR   0.030   0.002   TYR A 449 
 ARG   0.006   0.001   ARG H  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03413 (   77)
  hydrogen bonds       : angle       7.77165 (  171)
  SS BOND              : bond        0.00712 (    7)
  SS BOND              : angle       3.08245 (   14)
  covalent geometry    : bond        0.00346 ( 4273)
  covalent geometry    : angle       0.72487 ( 5805)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.438 
Fit side-chains
REVERT: H    3 GLN cc_start: 0.6457 (pp30) cc_final: 0.6231 (pp30)
REVERT: H   47 TRP cc_start: 0.5436 (t60) cc_final: 0.5153 (t60)
REVERT: B   95 TYR cc_start: 0.6174 (m-80) cc_final: 0.5865 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1744
  time to fit residues: 12.1494
Evaluate side-chains
  42 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0370
   chunk 24 optimal weight:    0.3980
   chunk 4 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 28 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
** L   3 GLN ** 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 = 0.3482 r_free = 0.3482 target = 0.050099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.041042 restraints weight = 37272.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.042262 restraints weight = 24927.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.043115 restraints weight = 18289.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5739
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4280  Z= 0.111
  Angle     :  0.673   6.801   5819  Z= 0.348
  Chirality :  0.047   0.242    616
  Planarity :  0.005   0.050    755
  Dihedral  :  5.813  30.302    599
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.32 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.14 (0.33), residues: 533
  helix: -3.40 (0.84), residues: 25
  sheet: -1.84 (0.40), residues: 139
  loop : -2.21 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 353 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.031   0.002   PHE L  98 
 TYR   0.020   0.002   TYR A 449 
 ARG   0.003   0.001   ARG B  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03141 (   77)
  hydrogen bonds       : angle       7.67003 (  171)
  SS BOND              : bond        0.00614 (    7)
  SS BOND              : angle       2.53364 (   14)
  covalent geometry    : bond        0.00255 ( 4273)
  covalent geometry    : angle       0.66227 ( 5805)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1952.34 seconds
wall clock time: 35 minutes 33.67 seconds (2133.67 seconds total)