Starting phenix.real_space_refine
on Thu Mar  6 00:36:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y0o_33551/03_2025/7y0o_33551.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y0o_33551/03_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_33551/03_2025/7y0o_33551.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y0o_33551/03_2025/7y0o_33551.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y0o_33551/03_2025/7y0o_33551.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y0o_33551/03_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-5624/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: 3.70, per 1000 atoms: 0.88
  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: 0.92
  Conformation dependent library (CDL) restraints added in 490.1 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: 0.49
  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: 0.98

  Time building geometry restraints manager: 1.12 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:             11.750
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.980
  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:             0.010
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.030
-------------------------------------------------------------------------------
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   4273  Z= 0.255
  Angle     :  0.927  12.762   5805  Z= 0.479
  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 

*********************** 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  : 0.501 
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: 0.1690
  time to fit residues: 12.9665
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  : 0.527 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3484 r_free = 0.3484 target = 0.050361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.041325 restraints weight = 37816.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.042465 restraints weight = 25832.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.043315 restraints weight = 19213.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5742
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4273  Z= 0.210
  Angle     :  0.686  10.422   5805  Z= 0.357
  Chirality :  0.046   0.165    616
  Planarity :  0.005   0.060    755
  Dihedral  :  6.218  28.692    599
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.19 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  8.14 %
    Favored  : 91.63 %
  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: -3.33 (0.32), residues: 533
  helix: -3.85 (0.75), residues: 31
  sheet: -2.14 (0.38), residues: 155
  loop : -2.16 (0.30), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.026   0.002   PHE L  98 
 TYR   0.022   0.002   TYR A 449 
 ARG   0.006   0.001   ARG A 355 

*********************** 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
  56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A  353 TRP cc_start: 0.4875 (p-90) cc_final: 0.4314 (p-90)
REVERT: H   48 MET cc_start: 0.6726 (mpp) cc_final: 0.6328 (mpp)
REVERT: L   38 GLN cc_start: 0.6702 (tp40) cc_final: 0.6067 (pt0)
REVERT: L   98 PHE cc_start: 0.4768 (m-10) cc_final: 0.4325 (m-80)
REVERT: B   34 MET cc_start: 0.6510 (mpp) cc_final: 0.5510 (tmm)
REVERT: B   36 TRP cc_start: 0.5766 (m100) cc_final: 0.5505 (m100)
REVERT: B   46 GLU cc_start: 0.6102 (tm-30) cc_final: 0.5723 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1891
  time to fit residues: 13.3552
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  : 0.493 
-------------------------------------------------------------------------------
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:    0.0070
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 2 optimal weight:    0.2980
   chunk 21 optimal weight:    0.4980
   overall best weight:    0.4198

-------------------------------------------------------------------------------
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 = 0.3505 r_free = 0.3505 target = 0.050795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.041282 restraints weight = 36599.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.042499 restraints weight = 25021.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.043438 restraints weight = 18441.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5750
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4273  Z= 0.159
  Angle     :  0.631   9.330   5805  Z= 0.329
  Chirality :  0.045   0.171    616
  Planarity :  0.005   0.054    755
  Dihedral  :  5.796  27.566    599
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.07 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  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: -3.23 (0.32), residues: 533
  helix: -3.61 (0.76), residues: 31
  sheet: -1.91 (0.40), residues: 149
  loop : -2.21 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  47 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.020   0.002   PHE L  98 
 TYR   0.032   0.002   TYR A 449 
 ARG   0.004   0.001   ARG H  50 

*********************** 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
  56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7638 (p90) cc_final: 0.7411 (p90)
REVERT: A  353 TRP cc_start: 0.4710 (p-90) cc_final: 0.4394 (p-90)
REVERT: H   48 MET cc_start: 0.6651 (mpp) cc_final: 0.6388 (mpp)
REVERT: L   98 PHE cc_start: 0.4620 (m-80) cc_final: 0.4334 (m-80)
REVERT: B   34 MET cc_start: 0.6750 (mpp) cc_final: 0.6520 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1538
  time to fit residues: 11.2795
Evaluate side-chains
  40 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 9 optimal weight:    0.1980
   chunk 3 optimal weight:    0.5980
   chunk 28 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    0.3980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.5982

-------------------------------------------------------------------------------
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**
B 116 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.050211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.041284 restraints weight = 37676.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.042474 restraints weight = 25508.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.043372 restraints weight = 18842.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5742
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4273  Z= 0.189
  Angle     :  0.660  11.365   5805  Z= 0.340
  Chirality :  0.045   0.178    616
  Planarity :  0.005   0.055    755
  Dihedral  :  5.838  27.272    599
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.76 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  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: -3.20 (0.32), residues: 533
  helix: -2.51 (1.20), residues: 19
  sheet: -2.00 (0.38), residues: 154
  loop : -2.28 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.018   0.002   PHE L  98 
 TYR   0.029   0.002   TYR A 449 
 ARG   0.005   0.001   ARG H  38 

*********************** 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
  55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7620 (p90) cc_final: 0.7240 (p90)
REVERT: H   47 TRP cc_start: 0.5570 (t60) cc_final: 0.5343 (t60)
REVERT: B   34 MET cc_start: 0.6737 (mpp) cc_final: 0.6484 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1719
  time to fit residues: 12.0022
Evaluate side-chains
  44 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0370
   chunk 3 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.6058

-------------------------------------------------------------------------------
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 = 0.050079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.041152 restraints weight = 38165.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.042354 restraints weight = 25546.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.043221 restraints weight = 18749.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5738
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4273  Z= 0.186
  Angle     :  0.660  11.513   5805  Z= 0.339
  Chirality :  0.046   0.180    616
  Planarity :  0.005   0.053    755
  Dihedral  :  5.872  27.488    599
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  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: -3.27 (0.32), residues: 533
  helix: -3.13 (0.96), residues: 25
  sheet: -2.11 (0.38), residues: 154
  loop : -2.22 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.013   0.002   PHE B 105 
 TYR   0.026   0.002   TYR A 449 
 ARG   0.005   0.001   ARG H  38 

*********************** 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
  52 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.523 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7607 (p90) cc_final: 0.7254 (p90)
REVERT: H    3 GLN cc_start: 0.6306 (pp30) cc_final: 0.6074 (pp30)
REVERT: H   47 TRP cc_start: 0.5662 (t60) cc_final: 0.5426 (t60)
REVERT: H   48 MET cc_start: 0.6777 (mpp) cc_final: 0.6530 (mpp)
REVERT: B   34 MET cc_start: 0.6888 (mpp) cc_final: 0.6436 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.2110
  time to fit residues: 13.9517
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  : 0.481 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 16 optimal weight:    0.0000
   chunk 2 optimal weight:    0.7980
   chunk 37 optimal weight:    0.3980
   chunk 14 optimal weight:    0.0270
   chunk 31 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0270
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.1900

-------------------------------------------------------------------------------
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 = 0.3508 r_free = 0.3508 target = 0.051025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.042072 restraints weight = 36784.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.043261 restraints weight = 24613.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.044164 restraints weight = 18049.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5715
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4273  Z= 0.135
  Angle     :  0.593   6.929   5805  Z= 0.309
  Chirality :  0.045   0.211    616
  Planarity :  0.004   0.050    755
  Dihedral  :  5.231  25.447    599
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.44 %
    Favored  : 91.56 %
  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: -3.02 (0.33), residues: 533
  helix: -3.07 (0.96), residues: 25
  sheet: -2.01 (0.38), residues: 155
  loop : -1.99 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  36 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.012   0.001   PHE A 400 
 TYR   0.017   0.001   TYR A 449 
 ARG   0.003   0.000   ARG B  19 

*********************** 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
  58 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.515 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7719 (p90) cc_final: 0.7217 (p90)
REVERT: H   47 TRP cc_start: 0.5727 (t60) cc_final: 0.5429 (t60)
REVERT: H   48 MET cc_start: 0.6851 (mpp) cc_final: 0.6587 (mpp)
REVERT: B   33 TYR cc_start: 0.3682 (m-10) cc_final: 0.3393 (m-10)
REVERT: B   34 MET cc_start: 0.6950 (mpp) cc_final: 0.6606 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2108
  time to fit residues: 15.0783
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  : 0.514 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 4 optimal weight:    0.0970
   chunk 25 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0570
   chunk 32 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.4696

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.050482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.041455 restraints weight = 37012.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.042627 restraints weight = 25067.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.043482 restraints weight = 18548.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5726
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4273  Z= 0.169
  Angle     :  0.651  10.558   5805  Z= 0.334
  Chirality :  0.046   0.203    616
  Planarity :  0.004   0.050    755
  Dihedral  :  5.591  25.500    599
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.13 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  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: -3.01 (0.33), residues: 533
  helix: -3.13 (0.94), residues: 25
  sheet: -1.94 (0.39), residues: 155
  loop : -2.01 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.010   0.002   PHE A 400 
 TYR   0.022   0.002   TYR A 449 
 ARG   0.004   0.001   ARG B  19 

*********************** 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
  60 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.523 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7644 (p90) cc_final: 0.7149 (p90)
REVERT: H   48 MET cc_start: 0.6733 (mpp) cc_final: 0.6508 (mpp)
REVERT: B   34 MET cc_start: 0.6634 (mpp) cc_final: 0.6231 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1825
  time to fit residues: 13.7741
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  : 0.487 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0270
   chunk 17 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 0 optimal weight:    1.0980
   chunk 23 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5638

-------------------------------------------------------------------------------
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 = 0.050516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.041318 restraints weight = 37297.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.042551 restraints weight = 24882.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.043454 restraints weight = 18206.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5743
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4273  Z= 0.182
  Angle     :  0.659  10.629   5805  Z= 0.339
  Chirality :  0.046   0.202    616
  Planarity :  0.004   0.050    755
  Dihedral  :  5.771  26.174    599
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.69 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  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: -3.06 (0.33), residues: 533
  helix: -3.39 (0.83), residues: 25
  sheet: -1.95 (0.38), residues: 154
  loop : -2.05 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP H  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.011   0.002   PHE B 105 
 TYR   0.022   0.002   TYR A 449 
 ARG   0.005   0.001   ARG H  50 

*********************** 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
  60 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7622 (p90) cc_final: 0.7072 (p90)
REVERT: H    3 GLN cc_start: 0.6457 (pp30) cc_final: 0.6249 (pp30)
REVERT: H   19 LYS cc_start: 0.5875 (tptp) cc_final: 0.5628 (tptp)
REVERT: B   34 MET cc_start: 0.6733 (mpp) cc_final: 0.6442 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2037
  time to fit residues: 15.1968
Evaluate side-chains
  46 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0870
   chunk 18 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.9760

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
H   1 GLN
** 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 = 0.3465 r_free = 0.3465 target = 0.049583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.040675 restraints weight = 37306.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.041861 restraints weight = 24966.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.042701 restraints weight = 18352.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5740
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4273  Z= 0.254
  Angle     :  0.763  13.682   5805  Z= 0.392
  Chirality :  0.049   0.219    616
  Planarity :  0.006   0.051    755
  Dihedral  :  6.474  27.046    599
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.20 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.04 %
    Favored  : 97.74 %
  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: -3.35 (0.32), residues: 533
  helix: -2.99 (1.08), residues: 19
  sheet: -2.21 (0.37), residues: 155
  loop : -2.30 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP B  36 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.023   0.003   PHE B 105 
 TYR   0.046   0.003   TYR A 449 
 ARG   0.007   0.001   ARG H  38 

*********************** 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
  54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7632 (p90) cc_final: 0.7122 (p90)
REVERT: H    1 GLN cc_start: 0.5876 (OUTLIER) cc_final: 0.5600 (pp30)
REVERT: H   47 TRP cc_start: 0.5620 (t60) cc_final: 0.5311 (t60)
REVERT: B   34 MET cc_start: 0.6154 (mpp) cc_final: 0.5407 (tmm)
REVERT: B   85 ARG cc_start: 0.7640 (tpm170) cc_final: 0.7333 (tpm170)
  outliers start: 1
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1901
  time to fit residues: 13.0447
Evaluate side-chains
  42 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 25 optimal weight:    0.0010
   chunk 0 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 1 optimal weight:    0.3980
   chunk 19 optimal weight:    0.0970
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0980
   overall best weight:    0.1984

-------------------------------------------------------------------------------
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
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3496 r_free = 0.3496 target = 0.050762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.041571 restraints weight = 36717.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.042769 restraints weight = 24585.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.043671 restraints weight = 18079.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5725
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   4273  Z= 0.152
  Angle     :  0.648   6.663   5805  Z= 0.337
  Chirality :  0.046   0.222    616
  Planarity :  0.004   0.048    755
  Dihedral  :  5.605  25.343    599
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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: -3.61 (0.71), residues: 31
  sheet: -1.91 (0.41), residues: 134
  loop : -2.20 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 353 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.015   0.001   PHE A 400 
 TYR   0.027   0.001   TYR A 449 
 ARG   0.003   0.000   ARG B  85 

********************** 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
  64 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7627 (p90) cc_final: 0.7023 (p90)
REVERT: B   33 TYR cc_start: 0.3509 (m-10) cc_final: 0.3219 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1663
  time to fit residues: 13.5652
Evaluate side-chains
  40 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0980
   chunk 4 optimal weight:    0.0870
   chunk 3 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 28 optimal weight:    7.9990
   chunk 5 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
** H   1 GLN ** 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 = 0.3484 r_free = 0.3484 target = 0.050300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.041401 restraints weight = 37187.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.042573 restraints weight = 24941.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.043428 restraints weight = 18318.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5722
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4273  Z= 0.180
  Angle     :  0.682   9.520   5805  Z= 0.351
  Chirality :  0.047   0.208    616
  Planarity :  0.004   0.048    755
  Dihedral  :  5.835  25.852    599
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.01 %
    Favored  : 87.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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: -3.26 (0.33), residues: 533
  helix: -3.64 (0.71), residues: 31
  sheet: -2.02 (0.38), residues: 144
  loop : -2.19 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.013   0.002   PHE B 105 
 TYR   0.035   0.002   TYR A 449 
 ARG   0.004   0.001   ARG B  85 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1848.19 seconds
wall clock time: 33 minutes 7.36 seconds (1987.36 seconds total)