Starting phenix.real_space_refine
on Thu Jun  5 20:24:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wxi_32880/06_2025/7wxi_32880.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wxi_32880/06_2025/7wxi_32880.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wxi_32880/06_2025/7wxi_32880.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wxi_32880/06_2025/7wxi_32880.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wxi_32880/06_2025/7wxi_32880.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wxi_32880/06_2025/7wxi_32880.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      30      5.16       5
     C    4064      2.51       5
     N    1174      2.21       5
     O    1252      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6522
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3247
          Classifications: {'peptide': 430}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 414}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Classifications: {'peptide': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.68, per 1000 atoms: 1.02
  Number of scatterers: 6522
  At special positions: 0
  Unit cell: (98.58, 92.22, 62.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       2     15.00
     O    1252      8.00
     N    1174      7.00
     C    4064      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.08
  Conformation dependent library (CDL) restraints added in 2.6 seconds
  

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  RGP A 801 "
        pdb=" CB  RGP B 801 "
  Number of C-beta restraints generated:  1596

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 12 sheets defined
      50.1% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 348 through 364
      removed outlier: 4.096A  pdb=" N   ALA A 364 " --> pdb=" O   ARG A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 384
    Processing helix  chain 'A' and resid 384 through 401
      removed outlier: 3.777A  pdb=" N   LYS A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 412
    Processing helix  chain 'A' and resid 415 through 433
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 495 through 513
      removed outlier: 4.331A  pdb=" N   VAL A 513 " --> pdb=" O   ALA A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 534
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 579 through 592
      removed outlier: 3.772A  pdb=" N   ALA A 583 " --> pdb=" O   ASP A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 613
    Processing helix  chain 'A' and resid 614 through 626
    Processing helix  chain 'A' and resid 633 through 640
    Processing helix  chain 'A' and resid 666 through 677
    Processing helix  chain 'A' and resid 689 through 700
      removed outlier: 3.626A  pdb=" N   ALA A 693 " --> pdb=" O   ASN A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 714
      removed outlier: 3.628A  pdb=" N   ALA A 714 " --> pdb=" O   SER A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 720
    Processing helix  chain 'A' and resid 739 through 744
    Processing helix  chain 'A' and resid 757 through 761
    Processing helix  chain 'B' and resid 348 through 364
      removed outlier: 4.096A  pdb=" N   ALA B 364 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 384
    Processing helix  chain 'B' and resid 384 through 401
      removed outlier: 3.777A  pdb=" N   LYS B 401 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 412
    Processing helix  chain 'B' and resid 415 through 433
    Processing helix  chain 'B' and resid 472 through 484
    Processing helix  chain 'B' and resid 495 through 513
      removed outlier: 4.331A  pdb=" N   VAL B 513 " --> pdb=" O   ALA B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 534
    Processing helix  chain 'B' and resid 546 through 557
    Processing helix  chain 'B' and resid 579 through 592
      removed outlier: 3.772A  pdb=" N   ALA B 583 " --> pdb=" O   ASP B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 613
    Processing helix  chain 'B' and resid 614 through 626
    Processing helix  chain 'B' and resid 633 through 640
    Processing helix  chain 'B' and resid 666 through 677
    Processing helix  chain 'B' and resid 689 through 700
      removed outlier: 3.626A  pdb=" N   ALA B 693 " --> pdb=" O   ASN B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 710 through 714
      removed outlier: 3.628A  pdb=" N   ALA B 714 " --> pdb=" O   SER B 711 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 716 through 720
    Processing helix  chain 'B' and resid 739 through 744
    Processing helix  chain 'B' and resid 757 through 761
    Processing sheet with id=AA1, first strand: chain 'A' and resid 750 through 751
      removed outlier: 4.420A  pdb=" N   GLU A 451 " --> pdb=" O   GLU A 751 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU A 450 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A 771 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 457
    Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 490
      removed outlier: 6.555A  pdb=" N   LEU A 462 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   LYS A 490 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   VAL A 464 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   LEU A 463 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 607
      removed outlier: 5.647A  pdb=" N   ILE A 606 " --> pdb=" O   VAL A 664 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 629 through 630
      removed outlier: 6.895A  pdb=" N   LYS A 629 " --> pdb=" O   CYS A 659 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 727 through 728
    Processing sheet with id=AA7, first strand: chain 'B' and resid 750 through 751
      removed outlier: 4.420A  pdb=" N   GLU B 451 " --> pdb=" O   GLU B 751 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU B 771 " --> pdb=" O   ARG B 445 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 457
    Processing sheet with id=AA9, first strand: chain 'B' and resid 487 through 490
      removed outlier: 6.555A  pdb=" N   LEU B 462 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   LYS B 490 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   VAL B 464 " --> pdb=" O   LYS B 490 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   LEU B 463 " --> pdb=" O   ILE B 542 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 605 through 607
      removed outlier: 5.647A  pdb=" N   ILE B 606 " --> pdb=" O   VAL B 664 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 629 through 630
      removed outlier: 6.895A  pdb=" N   LYS B 629 " --> pdb=" O   CYS B 659 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 727 through 728

    300 hydrogen bonds defined for protein.
    822 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.91

  Time building geometry restraints manager: 5.30 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1140
        1.31 -     1.43: 1536
        1.43 -     1.56: 3896
        1.56 -     1.68: 2
        1.68 -     1.81: 46
  Bond restraints: 6620
  Sorted by residual:
  bond pdb=" OE2 RGP A 801 "
       pdb=" PA  RGP A 801 "
    ideal  model  delta    sigma   weight residual
    1.798  1.646  0.152 2.00e-02 2.50e+03 5.78e+01
  bond pdb=" OE2 RGP B 801 "
       pdb=" PA  RGP B 801 "
    ideal  model  delta    sigma   weight residual
    1.798  1.646  0.152 2.00e-02 2.50e+03 5.78e+01
  bond pdb=" CD  RGP A 801 "
       pdb=" OE2 RGP A 801 "
    ideal  model  delta    sigma   weight residual
    1.302  1.395 -0.093 2.00e-02 2.50e+03 2.16e+01
  bond pdb=" CD  RGP B 801 "
       pdb=" OE2 RGP B 801 "
    ideal  model  delta    sigma   weight residual
    1.302  1.395 -0.093 2.00e-02 2.50e+03 2.16e+01
  bond pdb=" N   VAL A 455 "
       pdb=" CA  VAL A 455 "
    ideal  model  delta    sigma   weight residual
    1.459  1.437  0.022 1.25e-02 6.40e+03 3.13e+00
  ... (remaining 6615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 8772
        2.32 -     4.64: 150
        4.64 -     6.95: 34
        6.95 -     9.27: 6
        9.27 -    11.59: 2
  Bond angle restraints: 8964
  Sorted by residual:
  angle pdb=" OE2 RGP B 801 "
        pdb=" PA  RGP B 801 "
        pdb=" OA3 RGP B 801 "
      ideal   model   delta    sigma   weight residual
      97.78  109.37  -11.59 3.00e+00 1.11e-01 1.49e+01
  angle pdb=" OE2 RGP A 801 "
        pdb=" PA  RGP A 801 "
        pdb=" OA3 RGP A 801 "
      ideal   model   delta    sigma   weight residual
      97.78  109.37  -11.59 3.00e+00 1.11e-01 1.49e+01
  angle pdb=" CG  RGP B 801 "
        pdb=" CD  RGP B 801 "
        pdb=" OE2 RGP B 801 "
      ideal   model   delta    sigma   weight residual
     112.09  119.96   -7.87 3.00e+00 1.11e-01 6.89e+00
  angle pdb=" CG  RGP A 801 "
        pdb=" CD  RGP A 801 "
        pdb=" OE2 RGP A 801 "
      ideal   model   delta    sigma   weight residual
     112.09  119.96   -7.87 3.00e+00 1.11e-01 6.89e+00
  angle pdb=" N   ARG A 544 "
        pdb=" CA  ARG A 544 "
        pdb=" C   ARG A 544 "
      ideal   model   delta    sigma   weight residual
     114.75  111.53    3.22 1.26e+00 6.30e-01 6.53e+00
  ... (remaining 8959 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 3506
       16.01 -    32.02: 416
       32.02 -    48.02: 98
       48.02 -    64.03: 18
       64.03 -    80.04: 14
  Dihedral angle restraints: 4052
    sinusoidal: 1588
      harmonic: 2464
  Sorted by residual:
  dihedral pdb=" CA  ILE A 732 "
           pdb=" C   ILE A 732 "
           pdb=" N   HIS A 733 "
           pdb=" CA  HIS A 733 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.31   21.69     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CA  ILE B 732 "
           pdb=" C   ILE B 732 "
           pdb=" N   HIS B 733 "
           pdb=" CA  HIS B 733 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.31   21.69     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CA  THR A 366 "
           pdb=" C   THR A 366 "
           pdb=" N   PRO A 367 "
           pdb=" CA  PRO A 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.54  -21.46     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 4049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 562
       0.030 -    0.059: 276
       0.059 -    0.089: 136
       0.089 -    0.118: 52
       0.118 -    0.148: 22
  Chirality restraints: 1048
  Sorted by residual:
  chirality pdb=" CA  ILE A 574 "
            pdb=" N   ILE A 574 "
            pdb=" C   ILE A 574 "
            pdb=" CB  ILE A 574 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.45e-01
  chirality pdb=" CA  ILE B 574 "
            pdb=" N   ILE B 574 "
            pdb=" C   ILE B 574 "
            pdb=" CB  ILE B 574 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.45e-01
  chirality pdb=" CA  VAL B 519 "
            pdb=" N   VAL B 519 "
            pdb=" C   VAL B 519 "
            pdb=" CB  VAL B 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.95e-01
  ... (remaining 1045 not shown)

  Planarity restraints: 1174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 643 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO B 644 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 644 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 644 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 643 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO A 644 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 644 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 644 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 664 "    0.022 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO B 665 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 665 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 665 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1171 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 364
        2.70 -     3.25: 7708
        3.25 -     3.80: 10395
        3.80 -     4.35: 12380
        4.35 -     4.90: 20239
  Nonbonded interactions: 51086
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 429 "
            pdb=" OG  SER A 433 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" O   ILE B 429 "
            pdb=" OG  SER B 433 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" O   ALA A 509 "
            pdb=" OG1 THR A 512 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   ALA B 509 "
            pdb=" OG1 THR B 512 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   CYS B 570 "
            pdb=" ND1 HIS B 571 "
     model   vdw
     2.224 3.120
  ... (remaining 51081 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             32.940
  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:          0.360
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     35.670
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.090
  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:             0.020
  Load rotamer database and sin/cos tables:2.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   72.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
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      :  0.008   0.152   6620  Z= 0.363
  Angle     :  0.875  11.589   8964  Z= 0.460
  Chirality :  0.046   0.148   1048
  Planarity :  0.005   0.043   1174
  Dihedral  : 15.473  80.038   2456
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 24.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.22 %
    Favored  : 81.78 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 11.88 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.77 (0.24), residues: 856
  helix: -2.25 (0.22), residues: 354
  sheet: -4.26 (0.37), residues: 112
  loop : -3.68 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 748 
 HIS   0.007   0.002   HIS A 733 
 PHE   0.009   0.002   PHE B 387 
 TYR   0.011   0.002   TYR A 654 
 ARG   0.006   0.001   ARG B 551 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18356 (  300)
  hydrogen bonds       : angle       7.32348 (  822)
  covalent geometry    : bond        0.00762 ( 6620)
  covalent geometry    : angle       0.87497 ( 8964)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 PHE cc_start: 0.8727 (t80) cc_final: 0.8397 (t80)
REVERT: A  396 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8705 (pp)
REVERT: A  487 LEU cc_start: 0.8871 (tp) cc_final: 0.8670 (tp)
REVERT: A  505 LEU cc_start: 0.7996 (mt) cc_final: 0.7767 (mt)
REVERT: A  534 MET cc_start: 0.8501 (tmm) cc_final: 0.7827 (tmm)
REVERT: A  575 ASP cc_start: 0.8038 (t70) cc_final: 0.7835 (t70)
REVERT: A  577 ASP cc_start: 0.8501 (t70) cc_final: 0.8147 (t70)
REVERT: B  387 PHE cc_start: 0.8717 (t80) cc_final: 0.8386 (t80)
REVERT: B  505 LEU cc_start: 0.8076 (mt) cc_final: 0.7842 (mt)
REVERT: B  534 MET cc_start: 0.8501 (tmm) cc_final: 0.7814 (tmm)
REVERT: B  673 HIS cc_start: 0.8915 (t-90) cc_final: 0.8711 (t-170)
  outliers start: 4
  outliers final: 1
  residues processed: 135
  average time/residue: 0.2672
  time to fit residues: 46.5326
Evaluate side-chains
  94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 1.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    0.4980
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 78 optimal weight:    0.0000
   overall best weight:    0.8588

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 369 GLN
A 400 GLN
A 571 HIS
A 652 HIS
A 770 HIS
B 354 ASN
B 369 GLN
B 400 GLN
B 454 GLN
B 571 HIS
B 652 HIS
B 770 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.125197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.097345 restraints weight = 11606.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.100717 restraints weight = 7672.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.103224 restraints weight = 5765.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6620  Z= 0.155
  Angle     :  0.688   8.312   8964  Z= 0.360
  Chirality :  0.046   0.170   1048
  Planarity :  0.005   0.041   1174
  Dihedral  :  5.544  36.531    934
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.81 %
    Favored  : 92.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.27), residues: 856
  helix: -0.48 (0.25), residues: 372
  sheet: -3.65 (0.35), residues: 140
  loop : -3.01 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 768 
 HIS   0.007   0.001   HIS A 733 
 PHE   0.019   0.002   PHE A 760 
 TYR   0.008   0.001   TYR A 654 
 ARG   0.003   0.000   ARG B 585 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04482 (  300)
  hydrogen bonds       : angle       4.99453 (  822)
  covalent geometry    : bond        0.00340 ( 6620)
  covalent geometry    : angle       0.68822 ( 8964)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 147
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8275 (t0)
REVERT: A  487 LEU cc_start: 0.8511 (tp) cc_final: 0.8297 (tp)
REVERT: A  505 LEU cc_start: 0.8136 (mt) cc_final: 0.7853 (mt)
REVERT: A  724 GLU cc_start: 0.8652 (pp20) cc_final: 0.8336 (pt0)
REVERT: B  354 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8271 (t0)
REVERT: B  505 LEU cc_start: 0.8115 (mt) cc_final: 0.7850 (mt)
REVERT: B  662 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6770 (mm-30)
REVERT: B  724 GLU cc_start: 0.8646 (pp20) cc_final: 0.8316 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1504
  time to fit residues: 31.6341
Evaluate side-chains
  114 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0070
   chunk 80 optimal weight:    0.0570
   chunk 74 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.0122

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
B 354 ASN
** B 652 HIS ** 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 = 0.3676 r_free = 0.3676 target = 0.128642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.100800 restraints weight = 11527.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.104144 restraints weight = 7614.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.106574 restraints weight = 5708.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6620  Z= 0.151
  Angle     :  0.664   8.728   8964  Z= 0.339
  Chirality :  0.043   0.161   1048
  Planarity :  0.005   0.040   1174
  Dihedral  :  5.279  36.156    934
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  5.07 %
    Favored  : 94.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.29 (0.28), residues: 856
  helix:  0.16 (0.26), residues: 372
  sheet: -3.11 (0.36), residues: 142
  loop : -2.66 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 768 
 HIS   0.004   0.001   HIS A 673 
 PHE   0.014   0.002   PHE A 760 
 TYR   0.008   0.001   TYR A 573 
 ARG   0.003   0.000   ARG A 525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03890 (  300)
  hydrogen bonds       : angle       4.69555 (  822)
  covalent geometry    : bond        0.00335 ( 6620)
  covalent geometry    : angle       0.66353 ( 8964)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 150
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  487 LEU cc_start: 0.8420 (tp) cc_final: 0.8202 (tp)
REVERT: A  558 LEU cc_start: 0.6824 (tp) cc_final: 0.6086 (tp)
REVERT: B  505 LEU cc_start: 0.8049 (mt) cc_final: 0.7600 (mp)
REVERT: B  662 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6926 (mm-30)
REVERT: B  684 VAL cc_start: 0.9626 (p) cc_final: 0.9425 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1605
  time to fit residues: 34.8825
Evaluate side-chains
  115 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    0.0980
   chunk 74 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0470
   chunk 40 optimal weight:    0.0070
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.3096

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
B 354 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.132220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.102476 restraints weight = 11560.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.106457 restraints weight = 7123.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.109404 restraints weight = 5114.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6620  Z= 0.119
  Angle     :  0.660   8.861   8964  Z= 0.328
  Chirality :  0.043   0.154   1048
  Planarity :  0.004   0.040   1174
  Dihedral  :  4.974  35.583    934
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.84 (0.28), residues: 856
  helix:  0.48 (0.26), residues: 376
  sheet: -2.73 (0.36), residues: 140
  loop : -2.48 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 768 
 HIS   0.004   0.001   HIS B 673 
 PHE   0.018   0.002   PHE B 616 
 TYR   0.007   0.001   TYR A 654 
 ARG   0.009   0.000   ARG B 585 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03561 (  300)
  hydrogen bonds       : angle       4.40328 (  822)
  covalent geometry    : bond        0.00250 ( 6620)
  covalent geometry    : angle       0.65965 ( 8964)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  522 VAL cc_start: 0.9190 (p) cc_final: 0.8863 (p)
REVERT: B  505 LEU cc_start: 0.7839 (mt) cc_final: 0.7378 (mp)
REVERT: B  662 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6814 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1389
  time to fit residues: 32.9599
Evaluate side-chains
  120 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0060
   chunk 58 optimal weight:    6.9990
   chunk 75 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
B 354 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.133104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.102882 restraints weight = 11682.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.106747 restraints weight = 7347.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.109611 restraints weight = 5327.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6620  Z= 0.135
  Angle     :  0.698   9.436   8964  Z= 0.346
  Chirality :  0.045   0.206   1048
  Planarity :  0.005   0.038   1174
  Dihedral  :  5.073  35.102    934
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.65 (0.28), residues: 856
  helix:  0.59 (0.27), residues: 378
  sheet: -2.78 (0.36), residues: 132
  loop : -2.30 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 748 
 HIS   0.003   0.001   HIS B 673 
 PHE   0.020   0.001   PHE A 616 
 TYR   0.009   0.001   TYR B 654 
 ARG   0.008   0.000   ARG A 525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03332 (  300)
  hydrogen bonds       : angle       4.42492 (  822)
  covalent geometry    : bond        0.00300 ( 6620)
  covalent geometry    : angle       0.69842 ( 8964)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8654 (mm-30)
REVERT: A  570 CYS cc_start: 0.8159 (m) cc_final: 0.7931 (m)
REVERT: B  353 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8689 (mm-30)
REVERT: B  570 CYS cc_start: 0.8166 (m) cc_final: 0.7850 (m)
REVERT: B  662 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6813 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1241
  time to fit residues: 28.7994
Evaluate side-chains
  125 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 11 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 565 HIS
B 354 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.130822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.100690 restraints weight = 11764.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.104538 restraints weight = 7520.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.107246 restraints weight = 5501.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6620  Z= 0.150
  Angle     :  0.686  10.008   8964  Z= 0.341
  Chirality :  0.044   0.165   1048
  Planarity :  0.004   0.037   1174
  Dihedral  :  5.011  34.505    934
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.61 %
    Favored  : 97.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.43 (0.28), residues: 856
  helix:  0.82 (0.26), residues: 378
  sheet: -2.65 (0.37), residues: 132
  loop : -2.26 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 748 
 HIS   0.006   0.001   HIS A 733 
 PHE   0.018   0.001   PHE B 616 
 TYR   0.008   0.001   TYR A 573 
 ARG   0.005   0.000   ARG B 525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03266 (  300)
  hydrogen bonds       : angle       4.35739 (  822)
  covalent geometry    : bond        0.00343 ( 6620)
  covalent geometry    : angle       0.68614 ( 8964)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8697 (mm-30)
REVERT: A  503 MET cc_start: 0.8020 (tpp) cc_final: 0.7813 (tmm)
REVERT: B  353 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8699 (mm-30)
REVERT: B  428 GLN cc_start: 0.8814 (mp10) cc_final: 0.8609 (mp10)
REVERT: B  570 CYS cc_start: 0.8128 (m) cc_final: 0.7902 (m)
REVERT: B  662 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6997 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1270
  time to fit residues: 27.5622
Evaluate side-chains
  120 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 1 optimal weight:    0.6980
   chunk 81 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 428 GLN
A 565 HIS
B 354 ASN
** B 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.132348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.102712 restraints weight = 11670.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.106596 restraints weight = 7439.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.109397 restraints weight = 5425.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.4119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6620  Z= 0.128
  Angle     :  0.663   9.268   8964  Z= 0.329
  Chirality :  0.044   0.175   1048
  Planarity :  0.004   0.037   1174
  Dihedral  :  4.908  34.393    934
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.46 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.15 (0.29), residues: 856
  helix:  1.03 (0.27), residues: 378
  sheet: -2.41 (0.38), residues: 132
  loop : -2.12 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 748 
 HIS   0.005   0.001   HIS A 733 
 PHE   0.023   0.001   PHE A 616 
 TYR   0.007   0.001   TYR A 654 
 ARG   0.001   0.000   ARG B 525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03166 (  300)
  hydrogen bonds       : angle       4.24199 (  822)
  covalent geometry    : bond        0.00289 ( 6620)
  covalent geometry    : angle       0.66270 ( 8964)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8641 (mm-30)
REVERT: A  503 MET cc_start: 0.8062 (tpp) cc_final: 0.7746 (tmm)
REVERT: A  690 ASP cc_start: 0.7818 (p0) cc_final: 0.7614 (p0)
REVERT: B  353 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8671 (mm-30)
REVERT: B  505 LEU cc_start: 0.7881 (mt) cc_final: 0.7452 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1340
  time to fit residues: 29.0807
Evaluate side-chains
  116 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 565 HIS
B 354 ASN
B 565 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.132500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.102234 restraints weight = 11773.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.106106 restraints weight = 7547.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.108990 restraints weight = 5539.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.4309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6620  Z= 0.138
  Angle     :  0.700   9.562   8964  Z= 0.345
  Chirality :  0.045   0.170   1048
  Planarity :  0.004   0.035   1174
  Dihedral  :  4.942  34.275    934
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.72 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.10 (0.29), residues: 856
  helix:  1.00 (0.27), residues: 378
  sheet: -2.28 (0.39), residues: 132
  loop : -2.06 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 748 
 HIS   0.004   0.001   HIS A 733 
 PHE   0.020   0.002   PHE B 616 
 TYR   0.013   0.001   TYR B 654 
 ARG   0.002   0.000   ARG B 525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03226 (  300)
  hydrogen bonds       : angle       4.23705 (  822)
  covalent geometry    : bond        0.00317 ( 6620)
  covalent geometry    : angle       0.69983 ( 8964)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8652 (mm-30)
REVERT: A  616 PHE cc_start: 0.8694 (t80) cc_final: 0.8492 (t80)
REVERT: B  353 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8624 (mm-30)
REVERT: B  428 GLN cc_start: 0.8780 (mp10) cc_final: 0.8554 (mp10)
REVERT: B  505 LEU cc_start: 0.7921 (mt) cc_final: 0.7655 (mt)
REVERT: B  570 CYS cc_start: 0.8107 (m) cc_final: 0.7901 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1282
  time to fit residues: 27.2567
Evaluate side-chains
  117 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0870
   chunk 74 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
A 565 HIS
B 354 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.134438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.103986 restraints weight = 11857.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.108034 restraints weight = 7511.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.110989 restraints weight = 5470.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6620  Z= 0.127
  Angle     :  0.685   9.709   8964  Z= 0.341
  Chirality :  0.044   0.174   1048
  Planarity :  0.004   0.036   1174
  Dihedral  :  4.859  34.259    934
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.58 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.29), residues: 856
  helix:  1.07 (0.27), residues: 378
  sheet: -2.18 (0.40), residues: 132
  loop : -1.98 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 748 
 HIS   0.004   0.001   HIS A 733 
 PHE   0.012   0.001   PHE B 696 
 TYR   0.007   0.001   TYR A 573 
 ARG   0.001   0.000   ARG A 525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03119 (  300)
  hydrogen bonds       : angle       4.12440 (  822)
  covalent geometry    : bond        0.00289 ( 6620)
  covalent geometry    : angle       0.68498 ( 8964)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8629 (mm-30)
REVERT: A  626 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7899 (mm-30)
REVERT: B  353 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8619 (mm-30)
REVERT: B  505 LEU cc_start: 0.7910 (mt) cc_final: 0.7639 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1343
  time to fit residues: 28.6268
Evaluate side-chains
  115 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 71 optimal weight:    0.2980
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 38 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 565 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.133269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.103132 restraints weight = 11926.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.106909 restraints weight = 7656.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.109834 restraints weight = 5646.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6620  Z= 0.140
  Angle     :  0.697   9.246   8964  Z= 0.348
  Chirality :  0.045   0.172   1048
  Planarity :  0.004   0.036   1174
  Dihedral  :  4.856  34.114    934
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.29 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.29), residues: 856
  helix:  1.07 (0.27), residues: 378
  sheet: -2.13 (0.40), residues: 132
  loop : -1.93 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 768 
 HIS   0.004   0.001   HIS A 733 
 PHE   0.029   0.002   PHE A 616 
 TYR   0.009   0.001   TYR A 573 
 ARG   0.005   0.000   ARG B 625 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03086 (  300)
  hydrogen bonds       : angle       4.10580 (  822)
  covalent geometry    : bond        0.00320 ( 6620)
  covalent geometry    : angle       0.69660 ( 8964)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
REVERT: A  353 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8637 (mm-30)
REVERT: B  570 CYS cc_start: 0.8079 (m) cc_final: 0.7874 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1326
  time to fit residues: 26.8307
Evaluate side-chains
  110 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 35 optimal weight:    0.0370
   chunk 39 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0980
   chunk 53 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 42 optimal weight:   10.0000
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 565 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.136144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.106141 restraints weight = 11875.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.110146 restraints weight = 7559.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.113083 restraints weight = 5517.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.4803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6620  Z= 0.119
  Angle     :  0.675   9.082   8964  Z= 0.335
  Chirality :  0.044   0.170   1048
  Planarity :  0.004   0.036   1174
  Dihedral  :  4.724  34.119    934
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.29 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.29), residues: 856
  helix:  1.08 (0.27), residues: 378
  sheet: -2.03 (0.40), residues: 132
  loop : -1.79 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 768 
 HIS   0.004   0.001   HIS A 733 
 PHE   0.011   0.001   PHE A 696 
 TYR   0.013   0.001   TYR B 654 
 ARG   0.005   0.000   ARG B 625 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03019 (  300)
  hydrogen bonds       : angle       4.04553 (  822)
  covalent geometry    : bond        0.00268 ( 6620)
  covalent geometry    : angle       0.67513 ( 8964)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2898.04 seconds
wall clock time: 51 minutes 58.09 seconds (3118.09 seconds total)