Starting phenix.real_space_refine
on Tue Feb 11 05:13:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y0o_33551/02_2025/7y0o_33551.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y0o_33551/02_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_33551/02_2025/7y0o_33551.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y0o_33551/02_2025/7y0o_33551.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y0o_33551/02_2025/7y0o_33551.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y0o_33551/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.62, per 1000 atoms: 0.86
  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: 0.82
  Conformation dependent library (CDL) restraints added in 525.1 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: 0.44
  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: 0.96

  Time building geometry restraints manager: 1.00 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:             2.340
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.180
  Find NCS groups from input model:        0.060
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.600
-------------------------------------------------------------------------------
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  : 0.382 
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: 0.1553
  time to fit residues: 11.6042
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  : 0.412 
-------------------------------------------------------------------------------
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:    0.0670
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 = 0.3488 r_free = 0.3488 target = 0.050548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.041424 restraints weight = 37579.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.042590 restraints weight = 25580.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.043447 restraints weight = 18972.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5742
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4273  Z= 0.195
  Angle     :  0.671   9.884   5805  Z= 0.349
  Chirality :  0.046   0.168    616
  Planarity :  0.005   0.059    755
  Dihedral  :  6.084  28.446    599
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.38 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  7.47 %
    Favored  : 92.31 %
  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: -3.31 (0.32), residues: 533
  helix: -3.84 (0.72), residues: 32
  sheet: -2.09 (0.39), residues: 155
  loop : -2.16 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 353 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.028   0.002   PHE L  98 
 TYR   0.021   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
  57 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7781 (p90) cc_final: 0.7539 (p90)
REVERT: A  353 TRP cc_start: 0.4813 (p-90) cc_final: 0.4405 (p-90)
REVERT: H   48 MET cc_start: 0.6700 (mpp) cc_final: 0.6262 (mpp)
REVERT: L   98 PHE cc_start: 0.4805 (m-10) cc_final: 0.4308 (m-80)
REVERT: B   34 MET cc_start: 0.6583 (mpp) cc_final: 0.5576 (tmm)
REVERT: B   36 TRP cc_start: 0.5728 (m100) cc_final: 0.5503 (m100)
REVERT: B   46 GLU cc_start: 0.6108 (tm-30) cc_final: 0.5734 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1606
  time to fit residues: 11.7979
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  : 0.483 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 1 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0970
   chunk 38 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0770
   overall best weight:    0.3474

-------------------------------------------------------------------------------
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 = 0.3512 r_free = 0.3512 target = 0.051206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.041761 restraints weight = 37043.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.043007 restraints weight = 25103.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.043940 restraints weight = 18585.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5742
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   4273  Z= 0.150
  Angle     :  0.620   8.493   5805  Z= 0.323
  Chirality :  0.045   0.176    616
  Planarity :  0.004   0.053    755
  Dihedral  :  5.643  27.317    599
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.88 %
    Favored  : 91.93 %
  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: -3.17 (0.32), residues: 533
  helix: -3.66 (0.74), residues: 31
  sheet: -1.84 (0.40), residues: 149
  loop : -2.18 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  47 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.021   0.002   PHE L  98 
 TYR   0.030   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
  59 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7663 (p90) cc_final: 0.7393 (p90)
REVERT: A  353 TRP cc_start: 0.4725 (p-90) cc_final: 0.4434 (p-90)
REVERT: H   48 MET cc_start: 0.6630 (mpp) cc_final: 0.6412 (mpp)
REVERT: L   98 PHE cc_start: 0.4543 (m-80) cc_final: 0.4288 (m-80)
REVERT: B   34 MET cc_start: 0.6755 (mpp) cc_final: 0.6524 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2102
  time to fit residues: 16.2322
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  : 0.503 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    0.3980
   chunk 43 optimal weight:    4.9990
   chunk 9 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    0.2980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.5582

-------------------------------------------------------------------------------
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 = 0.3488 r_free = 0.3488 target = 0.050381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.041266 restraints weight = 36616.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.042460 restraints weight = 24856.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.043362 restraints weight = 18406.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5737
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4273  Z= 0.182
  Angle     :  0.654  11.139   5805  Z= 0.337
  Chirality :  0.045   0.180    616
  Planarity :  0.005   0.054    755
  Dihedral  :  5.738  26.819    599
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.76 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  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: -3.13 (0.32), residues: 533
  helix: -3.22 (0.94), residues: 25
  sheet: -1.94 (0.38), residues: 155
  loop : -2.14 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.019   0.002   PHE L  98 
 TYR   0.030   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
  56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.447 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7744 (p90) cc_final: 0.7352 (p90)
REVERT: H   48 MET cc_start: 0.6406 (mpp) cc_final: 0.6194 (mpp)
REVERT: B   34 MET cc_start: 0.6688 (mpp) cc_final: 0.6408 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1738
  time to fit residues: 12.4239
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  : 0.496 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 10 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0980
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0570
   chunk 3 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.4098

-------------------------------------------------------------------------------
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 = 0.3494 r_free = 0.3494 target = 0.050725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.041544 restraints weight = 38597.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.042784 restraints weight = 25620.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.043685 restraints weight = 18718.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5745
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   4273  Z= 0.155
  Angle     :  0.619   9.708   5805  Z= 0.319
  Chirality :  0.045   0.186    616
  Planarity :  0.004   0.051    755
  Dihedral  :  5.528  26.081    599
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.57 %
    Favored  : 90.43 %
  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: -3.06 (0.33), residues: 533
  helix: -3.10 (0.97), residues: 25
  sheet: -1.89 (0.38), residues: 154
  loop : -2.10 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  47 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.011   0.002   PHE L  98 
 TYR   0.024   0.001   TYR A 449 
 ARG   0.004   0.001   ARG B  85 

*********************** 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  : 0.463 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7798 (p90) cc_final: 0.7344 (p90)
REVERT: H   47 TRP cc_start: 0.5654 (t60) cc_final: 0.5395 (t60)
REVERT: B   34 MET cc_start: 0.6994 (mpp) cc_final: 0.6589 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1828
  time to fit residues: 12.4597
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  : 0.449 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0570
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.3481 r_free = 0.3481 target = 0.050192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.041303 restraints weight = 37619.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.042494 restraints weight = 25224.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.043357 restraints weight = 18544.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5742
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4273  Z= 0.195
  Angle     :  0.674  12.602   5805  Z= 0.346
  Chirality :  0.046   0.198    616
  Planarity :  0.005   0.053    755
  Dihedral  :  5.909  27.281    599
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.88 %
    Favored  : 89.12 %
  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: -3.14 (0.32), residues: 533
  helix: -2.48 (1.19), residues: 19
  sheet: -2.06 (0.37), residues: 159
  loop : -2.16 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.012   0.002   PHE B 105 
 TYR   0.026   0.002   TYR A 449 
 ARG   0.005   0.001   ARG H  38 

*********************** 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  : 0.523 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7643 (p90) cc_final: 0.7204 (p90)
REVERT: H   47 TRP cc_start: 0.5704 (t60) cc_final: 0.5410 (t60)
REVERT: B   34 MET cc_start: 0.6641 (mpp) cc_final: 0.6261 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1948
  time to fit residues: 14.3469
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  : 0.567 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 4 optimal weight:    0.0970
   chunk 25 optimal weight:    0.0270
   chunk 5 optimal weight:    0.0050
   chunk 40 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0470
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.0446

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.051955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.042805 restraints weight = 38177.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.043997 restraints weight = 25918.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.044873 restraints weight = 19233.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5737
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4273  Z= 0.137
  Angle     :  0.599   5.421   5805  Z= 0.312
  Chirality :  0.046   0.233    616
  Planarity :  0.004   0.048    755
  Dihedral  :  5.127  24.781    599
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  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: -3.01 (0.33), residues: 533
  helix: -3.46 (0.78), residues: 31
  sheet: -1.82 (0.39), residues: 155
  loop : -2.02 (0.30), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  36 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.018   0.001   PHE A 400 
 TYR   0.013   0.001   TYR A 449 
 ARG   0.004   0.000   ARG B  59 

*********************** 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
  64 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7674 (p90) cc_final: 0.7066 (p90)
REVERT: H   48 MET cc_start: 0.6962 (mpp) cc_final: 0.6741 (mpp)
REVERT: B    2 GLU cc_start: 0.5612 (mp0) cc_final: 0.5311 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1809
  time to fit residues: 14.6272
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  : 0.534 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 26 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3480 r_free = 0.3480 target = 0.050143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.041018 restraints weight = 35920.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.042192 restraints weight = 24500.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.043057 restraints weight = 18167.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5741
moved from start:          0.2646

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= 0.190
  Angle     :  0.691  16.883   5805  Z= 0.345
  Chirality :  0.047   0.206    616
  Planarity :  0.005   0.050    755
  Dihedral  :  5.715  26.217    599
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 13.28
  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: -3.14 (0.33), residues: 533
  helix: -3.10 (0.89), residues: 25
  sheet: -1.95 (0.39), residues: 155
  loop : -2.16 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP H  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.014   0.002   PHE A 342 
 TYR   0.024   0.002   TYR A 449 
 ARG   0.005   0.001   ARG H  38 

*********************** 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
  59 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7589 (p90) cc_final: 0.7074 (p90)
REVERT: B    2 GLU cc_start: 0.5194 (mp0) cc_final: 0.4826 (pm20)
REVERT: B   34 MET cc_start: 0.6726 (mpp) cc_final: 0.6347 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1790
  time to fit residues: 13.5491
Evaluate side-chains
  47 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3460 r_free = 0.3460 target = 0.049379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.040417 restraints weight = 37600.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.041590 restraints weight = 25233.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.042448 restraints weight = 18572.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5750
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4273  Z= 0.262
  Angle     :  0.819  22.312   5805  Z= 0.406
  Chirality :  0.049   0.210    616
  Planarity :  0.006   0.052    755
  Dihedral  :  6.545  27.350    599
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  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: -3.36 (0.32), residues: 533
  helix: -3.03 (1.07), residues: 19
  sheet: -1.95 (0.39), residues: 143
  loop : -2.45 (0.28), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP H  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.024   0.003   PHE L  98 
 TYR   0.030   0.003   TYR A 449 
 ARG   0.008   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: 0
    poor density    : 54
  time to evaluate  : 0.448 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7609 (p90) cc_final: 0.7120 (p90)
REVERT: H    3 GLN cc_start: 0.6545 (pp30) cc_final: 0.6320 (pp30)
REVERT: H   46 GLU cc_start: 0.6906 (mp0) cc_final: 0.6671 (pt0)
REVERT: H   50 ARG cc_start: 0.6616 (ttp80) cc_final: 0.4989 (ttp80)
REVERT: B    1 GLU cc_start: 0.4350 (pp20) cc_final: 0.4054 (pm20)
REVERT: B    2 GLU cc_start: 0.4498 (mp0) cc_final: 0.4198 (mp0)
REVERT: B   34 MET cc_start: 0.6213 (mpp) cc_final: 0.5402 (tmm)
REVERT: B   36 TRP cc_start: 0.5744 (m100) cc_final: 0.5003 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1878
  time to fit residues: 12.6913
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  : 0.444 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 12 optimal weight:    0.3980
   chunk 33 optimal weight:    6.9990
   chunk 29 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.050006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.040713 restraints weight = 37373.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.041915 restraints weight = 24854.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.042819 restraints weight = 18268.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5750
moved from start:          0.2959

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= 0.192
  Angle     :  0.726  17.199   5805  Z= 0.363
  Chirality :  0.047   0.210    616
  Planarity :  0.005   0.049    755
  Dihedral  :  6.088  26.058    599
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.44 %
    Favored  : 88.56 %
  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 : 0.00 %

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 (0.32), residues: 533
  helix: -2.69 (1.09), residues: 19
  sheet: -1.82 (0.39), residues: 137
  loop : -2.37 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.010   0.002   PHE A 400 
 TYR   0.036   0.002   TYR A 449 
 ARG   0.004   0.001   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
  61 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.554 
Fit side-chains
REVERT: H    3 GLN cc_start: 0.6555 (pp30) cc_final: 0.6319 (pp30)
REVERT: B    1 GLU cc_start: 0.4460 (pp20) cc_final: 0.4229 (pm20)
REVERT: B    2 GLU cc_start: 0.4448 (mp0) cc_final: 0.4083 (mp0)
REVERT: B   36 TRP cc_start: 0.5802 (m100) cc_final: 0.5473 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.2048
  time to fit residues: 15.4016
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  : 0.593 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3473 r_free = 0.3473 target = 0.049733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.040773 restraints weight = 36768.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.041957 restraints weight = 24599.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.042791 restraints weight = 18121.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5737
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4273  Z= 0.208
  Angle     :  0.747  19.034   5805  Z= 0.372
  Chirality :  0.048   0.200    616
  Planarity :  0.005   0.049    755
  Dihedral  :  6.269  26.304    599
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.01 %
    Favored  : 87.99 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.13 %
    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: -3.36 (0.32), residues: 533
  helix: -3.42 (0.83), residues: 25
  sheet: -1.90 (0.39), residues: 140
  loop : -2.42 (0.28), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.010   0.002   PHE A 486 
 TYR   0.040   0.002   TYR A 449 
 ARG   0.004   0.001   ARG H  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1732.16 seconds
wall clock time: 31 minutes 45.53 seconds (1905.53 seconds total)