Starting phenix.real_space_refine
on Thu Jun  5 18:30:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.cif"
  }
  resolution = 4.3
  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=   0.005
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      30      5.16       5
     C    4054      2.51       5
     N    1172      2.21       5
     O    1238      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6494
  Number of models: 1
  Model: ""
    Number of chains: 1
    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}
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.47, per 1000 atoms: 0.84
  Number of scatterers: 6494
  At special positions: 0
  Unit cell: (98.58, 94.34, 62.54, 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      30     16.00
     O    1238      8.00
     N    1172      7.00
     C    4054      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: 1.53
  Conformation dependent library (CDL) restraints added in 885.4 milliseconds
  

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1596

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      47.2% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 348 through 363
    Processing helix  chain 'A' and resid 368 through 384
    Processing helix  chain 'A' and resid 384 through 401
      removed outlier: 4.266A  pdb=" N   ILE A 388 " --> pdb=" O   ARG A 384 " (cutoff:3.500A)
      removed outlier: 4.158A  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 471 through 483
      removed outlier: 4.126A  pdb=" N   GLN A 475 " --> pdb=" O   ASP A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 513
      removed outlier: 3.629A  pdb=" N   THR A 512 " --> pdb=" O   GLU A 508 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   VAL A 513 " --> pdb=" O   ALA A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 534
      removed outlier: 3.792A  pdb=" N   LEU A 531 " --> pdb=" O   GLU A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 579 through 592
    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 678
    Processing helix  chain 'A' and resid 689 through 700
      removed outlier: 3.586A  pdb=" N   ALA A 693 " --> pdb=" O   ASN A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 742
      No H-bonds generated for 'chain 'A' and resid 740 through 742'
    Processing helix  chain 'A' and resid 757 through 761
    Processing helix  chain 'B' and resid 348 through 363
    Processing helix  chain 'B' and resid 368 through 384
    Processing helix  chain 'B' and resid 384 through 401
      removed outlier: 4.266A  pdb=" N   ILE B 388 " --> pdb=" O   ARG B 384 " (cutoff:3.500A)
      removed outlier: 4.158A  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 471 through 483
      removed outlier: 4.127A  pdb=" N   GLN B 475 " --> pdb=" O   ASP B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 513
      removed outlier: 3.629A  pdb=" N   THR B 512 " --> pdb=" O   GLU B 508 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   VAL B 513 " --> pdb=" O   ALA B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 534
      removed outlier: 3.792A  pdb=" N   LEU B 531 " --> pdb=" O   GLU B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 557
    Processing helix  chain 'B' and resid 579 through 592
    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 678
    Processing helix  chain 'B' and resid 689 through 700
      removed outlier: 3.586A  pdb=" N   ALA B 693 " --> pdb=" O   ASN B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 740 through 742
      No H-bonds generated for 'chain 'B' and resid 740 through 742'
    Processing helix  chain 'B' and resid 757 through 761
    Processing sheet with id=AA1, first strand: chain 'A' and resid 744 through 750
      removed outlier: 7.301A  pdb=" N   LEU A 450 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   THR A 456 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   VAL A 440 " --> pdb=" O   THR A 456 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ARG A 445 " --> pdb=" O   GLU A 771 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLU A 771 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 490
      removed outlier: 6.479A  pdb=" N   LEU A 462 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   LYS A 490 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   VAL A 464 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   VAL A 461 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   ILE A 542 " --> pdb=" O   VAL A 461 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   LEU A 463 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574
      removed outlier: 7.447A  pdb=" N   ILE A 574 " --> pdb=" O   HIS A 607 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ILE A 606 " --> pdb=" O   VAL A 664 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 630
      removed outlier: 6.625A  pdb=" N   LYS A 629 " --> pdb=" O   CYS A 659 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 726 through 728
      removed outlier: 4.272A  pdb=" N   GLY A 726 " --> pdb=" O   VAL A 738 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 744 through 750
      removed outlier: 7.300A  pdb=" N   LEU B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   THR B 456 " --> pdb=" O   VAL B 440 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   VAL B 440 " --> pdb=" O   THR B 456 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ARG B 445 " --> pdb=" O   GLU B 771 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLU B 771 " --> pdb=" O   ARG B 445 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 487 through 490
      removed outlier: 6.478A  pdb=" N   LEU B 462 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   LYS B 490 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   VAL B 464 " --> pdb=" O   LYS B 490 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   VAL B 461 " --> pdb=" O   LEU B 540 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   ILE B 542 " --> pdb=" O   VAL B 461 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LEU B 463 " --> pdb=" O   ILE B 542 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 573 through 574
      removed outlier: 7.447A  pdb=" N   ILE B 574 " --> pdb=" O   HIS B 607 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ILE B 606 " --> pdb=" O   VAL B 664 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 629 through 630
      removed outlier: 6.625A  pdb=" N   LYS B 629 " --> pdb=" O   CYS B 659 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 726 through 728
      removed outlier: 4.273A  pdb=" N   GLY B 726 " --> pdb=" O   VAL B 738 " (cutoff:3.500A)

    290 hydrogen bonds defined for protein.
    840 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: 3.63

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2260
        1.34 -     1.46: 1115
        1.46 -     1.57: 3173
        1.57 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 6594
  Sorted by residual:
  bond pdb=" C   LYS B 629 "
       pdb=" N   ILE B 630 "
    ideal  model  delta    sigma   weight residual
    1.330  1.311  0.020 1.42e-02 4.96e+03 1.91e+00
  bond pdb=" C   ARG A 411 "
       pdb=" N   LEU A 412 "
    ideal  model  delta    sigma   weight residual
    1.334  1.316  0.019 1.38e-02 5.25e+03 1.85e+00
  bond pdb=" CG  LEU B 389 "
       pdb=" CD1 LEU B 389 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.79e+00
  bond pdb=" CG  LEU A 389 "
       pdb=" CD1 LEU A 389 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.79e+00
  bond pdb=" CA  GLY A 764 "
       pdb=" C   GLY A 764 "
    ideal  model  delta    sigma   weight residual
    1.519  1.509  0.009 7.00e-03 2.04e+04 1.78e+00
  ... (remaining 6589 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.61: 8875
        3.61 -     7.22: 49
        7.22 -    10.84: 2
       10.84 -    14.45: 0
       14.45 -    18.06: 2
  Bond angle restraints: 8928
  Sorted by residual:
  angle pdb=" CA  LEU A 389 "
        pdb=" CB  LEU A 389 "
        pdb=" CG  LEU A 389 "
      ideal   model   delta    sigma   weight residual
     116.30  134.36  -18.06 3.50e+00 8.16e-02 2.66e+01
  angle pdb=" CA  LEU B 389 "
        pdb=" CB  LEU B 389 "
        pdb=" CG  LEU B 389 "
      ideal   model   delta    sigma   weight residual
     116.30  134.34  -18.04 3.50e+00 8.16e-02 2.66e+01
  angle pdb=" C   LEU B 389 "
        pdb=" N   ASP B 390 "
        pdb=" CA  ASP B 390 "
      ideal   model   delta    sigma   weight residual
     120.29  115.40    4.89 1.42e+00 4.96e-01 1.19e+01
  angle pdb=" C   LEU A 389 "
        pdb=" N   ASP A 390 "
        pdb=" CA  ASP A 390 "
      ideal   model   delta    sigma   weight residual
     120.29  115.43    4.86 1.42e+00 4.96e-01 1.17e+01
  angle pdb=" CA  GLU A 526 "
        pdb=" CB  GLU A 526 "
        pdb=" CG  GLU A 526 "
      ideal   model   delta    sigma   weight residual
     114.10  107.76    6.34 2.00e+00 2.50e-01 1.00e+01
  ... (remaining 8923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.78: 3517
       14.78 -    29.57: 376
       29.57 -    44.35: 111
       44.35 -    59.13: 28
       59.13 -    73.92: 4
  Dihedral angle restraints: 4036
    sinusoidal: 1572
      harmonic: 2464
  Sorted by residual:
  dihedral pdb=" CA  GLN B 638 "
           pdb=" C   GLN B 638 "
           pdb=" N   GLN B 639 "
           pdb=" CA  GLN B 639 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.90  -18.10     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  GLN A 638 "
           pdb=" C   GLN A 638 "
           pdb=" N   GLN A 639 "
           pdb=" CA  GLN A 639 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.94  -18.06     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  THR A 524 "
           pdb=" C   THR A 524 "
           pdb=" N   ARG A 525 "
           pdb=" CA  ARG A 525 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.27   15.73     0      5.00e+00 4.00e-02 9.89e+00
  ... (remaining 4033 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 564
       0.028 -    0.057: 286
       0.057 -    0.085: 136
       0.085 -    0.113: 49
       0.113 -    0.142: 11
  Chirality restraints: 1046
  Sorted by residual:
  chirality pdb=" CB  ILE B 560 "
            pdb=" CA  ILE B 560 "
            pdb=" CG1 ILE B 560 "
            pdb=" CG2 ILE B 560 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CB  ILE A 560 "
            pdb=" CA  ILE A 560 "
            pdb=" CG1 ILE A 560 "
            pdb=" CG2 ILE A 560 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  ILE B 685 "
            pdb=" N   ILE B 685 "
            pdb=" C   ILE B 685 "
            pdb=" CB  ILE B 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 1043 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 526 "   -0.007 2.00e-02 2.50e+03   1.52e-02 2.32e+00
        pdb=" CD  GLU B 526 "    0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 526 "   -0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 526 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 526 "    0.007 2.00e-02 2.50e+03   1.52e-02 2.30e+00
        pdb=" CD  GLU A 526 "   -0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 526 "    0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 526 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 579 "   -0.006 2.00e-02 2.50e+03   1.30e-02 1.70e+00
        pdb=" CG  ASP A 579 "    0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 579 "   -0.008 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 579 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 185
        2.63 -     3.20: 7118
        3.20 -     3.77: 10311
        3.77 -     4.33: 13524
        4.33 -     4.90: 21586
  Nonbonded interactions: 52724
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 546 "
            pdb=" OD1 ASP A 548 "
     model   vdw
     2.067 3.040
  nonbonded pdb=" OG  SER B 546 "
            pdb=" OD1 ASP B 548 "
     model   vdw
     2.068 3.040
  nonbonded pdb=" O   ASN B 672 "
            pdb=" OG1 THR B 676 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" O   ASN A 672 "
            pdb=" OG1 THR A 676 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" O   ARG B 356 "
            pdb=" OG  SER B 359 "
     model   vdw
     2.105 3.040
  ... (remaining 52719 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: 0.03
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:             1.130
  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:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.550
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   6594  Z= 0.320
  Angle     :  0.864  18.061   8928  Z= 0.489
  Chirality :  0.042   0.142   1046
  Planarity :  0.004   0.032   1170
  Dihedral  : 14.117  73.918   2440
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 26.18
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 11.45 %
    Favored  : 88.32 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  8.41 %
    Favored  : 89.86 %
  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: -4.55 (0.24), residues: 856
  helix: -2.05 (0.22), residues: 352
  sheet: -3.02 (0.39), residues: 144
  loop : -3.99 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 768 
 HIS   0.007   0.002   HIS B 565 
 PHE   0.015   0.003   PHE B 706 
 TYR   0.009   0.001   TYR B 654 
 ARG   0.005   0.001   ARG B 735 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16148 (  290)
  hydrogen bonds       : angle       7.01021 (  840)
  covalent geometry    : bond        0.00621 ( 6594)
  covalent geometry    : angle       0.86356 ( 8928)

*********************** 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
  214 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 202
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 PHE cc_start: 0.9250 (t80) cc_final: 0.8741 (t80)
REVERT: A  452 LEU cc_start: 0.9225 (tp) cc_final: 0.8886 (tt)
REVERT: A  481 MET cc_start: 0.8116 (mtp) cc_final: 0.7595 (mtp)
REVERT: A  488 LEU cc_start: 0.9382 (tp) cc_final: 0.9141 (tp)
REVERT: A  540 LEU cc_start: 0.9448 (tp) cc_final: 0.9149 (tp)
REVERT: A  577 ASP cc_start: 0.8891 (t70) cc_final: 0.8655 (t0)
REVERT: A  606 ILE cc_start: 0.9502 (mp) cc_final: 0.9283 (tp)
REVERT: A  652 HIS cc_start: 0.9092 (t70) cc_final: 0.8428 (t70)
REVERT: A  654 TYR cc_start: 0.8488 (m-80) cc_final: 0.7557 (m-10)
REVERT: A  677 TYR cc_start: 0.8726 (m-80) cc_final: 0.8272 (m-80)
REVERT: A  701 ASP cc_start: 0.8553 (p0) cc_final: 0.8285 (p0)
REVERT: A  713 PHE cc_start: 0.8636 (m-80) cc_final: 0.8382 (m-80)
REVERT: B  363 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8773 (tp40)
REVERT: B  387 PHE cc_start: 0.9131 (t80) cc_final: 0.8805 (t80)
REVERT: B  451 GLU cc_start: 0.7736 (mm-30) cc_final: 0.6904 (pm20)
REVERT: B  481 MET cc_start: 0.8014 (mtp) cc_final: 0.7553 (mtp)
REVERT: B  488 LEU cc_start: 0.9239 (tp) cc_final: 0.8933 (tp)
REVERT: B  504 GLU cc_start: 0.9233 (mt-10) cc_final: 0.9014 (pt0)
REVERT: B  521 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8923 (tt)
REVERT: B  582 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8809 (mmtm)
REVERT: B  584 LEU cc_start: 0.9233 (mt) cc_final: 0.9020 (mt)
REVERT: B  601 MET cc_start: 0.8163 (ppp) cc_final: 0.7718 (ptt)
REVERT: B  606 ILE cc_start: 0.9494 (mp) cc_final: 0.9288 (tp)
REVERT: B  616 PHE cc_start: 0.8115 (t80) cc_final: 0.7906 (t80)
REVERT: B  620 CYS cc_start: 0.9165 (m) cc_final: 0.8922 (m)
REVERT: B  654 TYR cc_start: 0.8375 (m-80) cc_final: 0.8046 (m-10)
REVERT: B  677 TYR cc_start: 0.8784 (m-80) cc_final: 0.8350 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 208
  average time/residue: 0.2192
  time to fit residues: 57.5352
Evaluate side-chains
  146 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 137
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 65 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 43 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 67 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 40 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.8388

-------------------------------------------------------------------------------
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 497 HIS
A 556 GLN
A 565 HIS
A 599 ASN
A 607 HIS
A 621 ASN
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 675 HIS
** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 ASN
** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 369 GLN
B 449 GLN
B 497 HIS
B 565 HIS
B 599 ASN
B 607 HIS
B 621 ASN
B 675 HIS
** B 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.092628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.072504 restraints weight = 19868.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.075029 restraints weight = 12939.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.076916 restraints weight = 9554.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6594  Z= 0.166
  Angle     :  0.662   7.689   8928  Z= 0.348
  Chirality :  0.044   0.146   1046
  Planarity :  0.004   0.041   1170
  Dihedral  :  5.073  17.231    918
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  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: -2.94 (0.27), residues: 856
  helix: -0.30 (0.26), residues: 344
  sheet: -2.65 (0.40), residues: 146
  loop : -3.31 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 748 
 HIS   0.005   0.001   HIS A 565 
 PHE   0.012   0.002   PHE B 760 
 TYR   0.005   0.001   TYR A 654 
 ARG   0.006   0.001   ARG A 718 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04176 (  290)
  hydrogen bonds       : angle       5.41903 (  840)
  covalent geometry    : bond        0.00364 ( 6594)
  covalent geometry    : angle       0.66216 ( 8928)

*********************** 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
  187 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.772 
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: 0.9120 (t80) cc_final: 0.8897 (t80)
REVERT: A  389 LEU cc_start: 0.9429 (pp) cc_final: 0.9214 (mp)
REVERT: A  481 MET cc_start: 0.8100 (mtp) cc_final: 0.7643 (mtp)
REVERT: A  488 LEU cc_start: 0.9368 (tp) cc_final: 0.9090 (tp)
REVERT: A  571 HIS cc_start: 0.8430 (m90) cc_final: 0.8119 (m90)
REVERT: A  574 ILE cc_start: 0.9572 (mt) cc_final: 0.9118 (tp)
REVERT: A  575 ASP cc_start: 0.9125 (t0) cc_final: 0.8666 (t0)
REVERT: A  677 TYR cc_start: 0.8753 (m-80) cc_final: 0.8129 (m-80)
REVERT: A  713 PHE cc_start: 0.8542 (m-80) cc_final: 0.8326 (m-80)
REVERT: B  363 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8537 (tp40)
REVERT: B  387 PHE cc_start: 0.9042 (t80) cc_final: 0.8673 (t80)
REVERT: B  451 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7090 (pm20)
REVERT: B  481 MET cc_start: 0.8163 (mtp) cc_final: 0.7847 (mtp)
REVERT: B  488 LEU cc_start: 0.9169 (tp) cc_final: 0.8856 (tp)
REVERT: B  575 ASP cc_start: 0.9069 (t0) cc_final: 0.8544 (t0)
REVERT: B  601 MET cc_start: 0.8360 (ppp) cc_final: 0.7177 (tmm)
REVERT: B  654 TYR cc_start: 0.8690 (m-80) cc_final: 0.7215 (m-10)
REVERT: B  677 TYR cc_start: 0.8823 (m-80) cc_final: 0.8156 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1633
  time to fit residues: 41.3542
Evaluate side-chains
  150 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0270
   chunk 29 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.1440

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

Flipped N/Q/H residues before XYZ refinement:
A 449 GLN
A 497 HIS
A 499 ASN
B 497 HIS
B 499 ASN
B 556 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.095190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.075093 restraints weight = 19298.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.077742 restraints weight = 12413.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.079663 restraints weight = 9077.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6594  Z= 0.126
  Angle     :  0.608   5.921   8928  Z= 0.320
  Chirality :  0.043   0.144   1046
  Planarity :  0.004   0.042   1170
  Dihedral  :  4.686  15.705    918
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  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: -2.38 (0.28), residues: 856
  helix:  0.22 (0.27), residues: 358
  sheet: -2.27 (0.43), residues: 134
  loop : -3.24 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 748 
 HIS   0.002   0.001   HIS A 497 
 PHE   0.019   0.002   PHE B 387 
 TYR   0.005   0.001   TYR A 654 
 ARG   0.004   0.000   ARG A 718 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03450 (  290)
  hydrogen bonds       : angle       4.93243 (  840)
  covalent geometry    : bond        0.00273 ( 6594)
  covalent geometry    : angle       0.60843 ( 8928)

*********************** 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
  186 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  481 MET cc_start: 0.7998 (mtp) cc_final: 0.7544 (mtp)
REVERT: A  488 LEU cc_start: 0.9347 (tp) cc_final: 0.9119 (tp)
REVERT: A  504 GLU cc_start: 0.9476 (mt-10) cc_final: 0.9216 (mp0)
REVERT: A  534 MET cc_start: 0.8795 (tpp) cc_final: 0.8306 (tpp)
REVERT: A  571 HIS cc_start: 0.8413 (m90) cc_final: 0.8072 (m90)
REVERT: A  574 ILE cc_start: 0.9590 (mt) cc_final: 0.9153 (tp)
REVERT: A  575 ASP cc_start: 0.9044 (t0) cc_final: 0.8654 (t0)
REVERT: A  603 THR cc_start: 0.9155 (t) cc_final: 0.8646 (t)
REVERT: A  658 GLU cc_start: 0.8820 (mp0) cc_final: 0.8612 (mp0)
REVERT: A  677 TYR cc_start: 0.8743 (m-80) cc_final: 0.8068 (m-80)
REVERT: B  363 GLN cc_start: 0.8970 (tp-100) cc_final: 0.8751 (tp40)
REVERT: B  389 LEU cc_start: 0.8848 (mp) cc_final: 0.8424 (pp)
REVERT: B  451 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7335 (pm20)
REVERT: B  481 MET cc_start: 0.8112 (mtp) cc_final: 0.7663 (mtp)
REVERT: B  488 LEU cc_start: 0.9173 (tp) cc_final: 0.8903 (tp)
REVERT: B  504 GLU cc_start: 0.9577 (pt0) cc_final: 0.9330 (pp20)
REVERT: B  534 MET cc_start: 0.8637 (tpp) cc_final: 0.7922 (tpp)
REVERT: B  558 LEU cc_start: 0.9189 (mt) cc_final: 0.8754 (mt)
REVERT: B  571 HIS cc_start: 0.8552 (m90) cc_final: 0.8275 (m90)
REVERT: B  575 ASP cc_start: 0.8952 (t0) cc_final: 0.8453 (t0)
REVERT: B  582 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8762 (mmmt)
REVERT: B  651 LYS cc_start: 0.9427 (mttm) cc_final: 0.9180 (mmtm)
REVERT: B  654 TYR cc_start: 0.7953 (m-80) cc_final: 0.7688 (m-10)
REVERT: B  677 TYR cc_start: 0.8875 (m-80) cc_final: 0.8074 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1527
  time to fit residues: 38.5987
Evaluate side-chains
  149 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 56 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 43 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 497 HIS
B 497 HIS
B 652 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.094163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.074418 restraints weight = 19911.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.077082 restraints weight = 12894.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.078999 restraints weight = 9423.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6594  Z= 0.146
  Angle     :  0.598   5.233   8928  Z= 0.312
  Chirality :  0.043   0.140   1046
  Planarity :  0.004   0.044   1170
  Dihedral  :  4.544  15.645    918
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  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: -2.03 (0.28), residues: 856
  helix:  0.53 (0.27), residues: 360
  sheet: -2.19 (0.44), residues: 136
  loop : -3.03 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 768 
 HIS   0.004   0.001   HIS A 497 
 PHE   0.014   0.002   PHE A 616 
 TYR   0.008   0.001   TYR A 654 
 ARG   0.003   0.000   ARG B 731 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03231 (  290)
  hydrogen bonds       : angle       4.76216 (  840)
  covalent geometry    : bond        0.00316 ( 6594)
  covalent geometry    : angle       0.59807 ( 8928)

*********************** 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
  174 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  481 MET cc_start: 0.7947 (mtp) cc_final: 0.7547 (mtp)
REVERT: A  488 LEU cc_start: 0.9289 (tp) cc_final: 0.8993 (tp)
REVERT: A  528 ILE cc_start: 0.9138 (tp) cc_final: 0.8858 (pt)
REVERT: A  534 MET cc_start: 0.8794 (tpp) cc_final: 0.8297 (tpp)
REVERT: A  571 HIS cc_start: 0.8486 (m90) cc_final: 0.8148 (m90)
REVERT: A  574 ILE cc_start: 0.9656 (mt) cc_final: 0.9208 (tp)
REVERT: A  575 ASP cc_start: 0.8918 (t0) cc_final: 0.8551 (t0)
REVERT: A  654 TYR cc_start: 0.7634 (m-10) cc_final: 0.7348 (m-10)
REVERT: A  677 TYR cc_start: 0.8688 (m-80) cc_final: 0.8084 (m-80)
REVERT: B  363 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8272 (tp40)
REVERT: B  389 LEU cc_start: 0.8995 (mp) cc_final: 0.8671 (pp)
REVERT: B  481 MET cc_start: 0.8226 (mtp) cc_final: 0.7781 (mtp)
REVERT: B  488 LEU cc_start: 0.9121 (tp) cc_final: 0.8785 (tp)
REVERT: B  528 ILE cc_start: 0.9017 (tp) cc_final: 0.8735 (pt)
REVERT: B  537 HIS cc_start: 0.8714 (m90) cc_final: 0.8390 (m90)
REVERT: B  551 ARG cc_start: 0.9499 (mmm-85) cc_final: 0.9265 (mmm-85)
REVERT: B  558 LEU cc_start: 0.9198 (mt) cc_final: 0.8771 (mt)
REVERT: B  571 HIS cc_start: 0.8522 (m90) cc_final: 0.8225 (m90)
REVERT: B  575 ASP cc_start: 0.8866 (t0) cc_final: 0.8378 (t0)
REVERT: B  651 LYS cc_start: 0.9456 (mttm) cc_final: 0.9099 (mmtm)
REVERT: B  677 TYR cc_start: 0.8763 (m-80) cc_final: 0.7981 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.1594
  time to fit residues: 37.7469
Evaluate side-chains
  144 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 79 optimal weight:    7.9990
   chunk 54 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0370
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 80 optimal weight:    0.1980
   chunk 37 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.7060

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

Flipped N/Q/H residues before XYZ refinement:
A 497 HIS
B 354 ASN
B 497 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.097454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.078101 restraints weight = 19340.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.080863 restraints weight = 12312.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.082873 restraints weight = 8877.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6594  Z= 0.105
  Angle     :  0.584   7.492   8928  Z= 0.300
  Chirality :  0.042   0.139   1046
  Planarity :  0.004   0.043   1170
  Dihedral  :  4.285  17.221    918
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  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: -1.79 (0.29), residues: 856
  helix:  0.82 (0.28), residues: 348
  sheet: -2.29 (0.42), residues: 144
  loop : -2.78 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 748 
 HIS   0.003   0.001   HIS A 497 
 PHE   0.009   0.001   PHE A 387 
 TYR   0.006   0.001   TYR B 654 
 ARG   0.004   0.000   ARG A 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03022 (  290)
  hydrogen bonds       : angle       4.54694 (  840)
  covalent geometry    : bond        0.00229 ( 6594)
  covalent geometry    : angle       0.58438 ( 8928)

*********************** 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
  192 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 LEU cc_start: 0.9371 (pp) cc_final: 0.9042 (mm)
REVERT: A  451 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7538 (mm-30)
REVERT: A  481 MET cc_start: 0.7952 (mtp) cc_final: 0.7636 (mtp)
REVERT: A  488 LEU cc_start: 0.9341 (tp) cc_final: 0.9138 (tp)
REVERT: A  504 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8950 (tm-30)
REVERT: A  528 ILE cc_start: 0.9086 (tp) cc_final: 0.8876 (pt)
REVERT: A  534 MET cc_start: 0.8724 (tpp) cc_final: 0.8313 (tpp)
REVERT: A  571 HIS cc_start: 0.8420 (m90) cc_final: 0.8119 (m90)
REVERT: A  574 ILE cc_start: 0.9623 (mt) cc_final: 0.9155 (tp)
REVERT: A  575 ASP cc_start: 0.8826 (t0) cc_final: 0.8543 (t0)
REVERT: A  660 CYS cc_start: 0.8467 (m) cc_final: 0.8023 (m)
REVERT: A  677 TYR cc_start: 0.8620 (m-80) cc_final: 0.8001 (m-80)
REVERT: A  704 CYS cc_start: 0.8192 (p) cc_final: 0.7957 (p)
REVERT: B  363 GLN cc_start: 0.8875 (tp-100) cc_final: 0.8614 (tp40)
REVERT: B  481 MET cc_start: 0.8170 (mtp) cc_final: 0.7814 (mtp)
REVERT: B  488 LEU cc_start: 0.9119 (tp) cc_final: 0.8857 (tp)
REVERT: B  516 GLU cc_start: 0.7185 (tt0) cc_final: 0.6856 (tt0)
REVERT: B  534 MET cc_start: 0.8704 (tpp) cc_final: 0.8322 (tpp)
REVERT: B  551 ARG cc_start: 0.9474 (mmm-85) cc_final: 0.9225 (mmm-85)
REVERT: B  571 HIS cc_start: 0.8443 (m90) cc_final: 0.8113 (m90)
REVERT: B  575 ASP cc_start: 0.8787 (t0) cc_final: 0.8277 (t0)
REVERT: B  601 MET cc_start: 0.8079 (ppp) cc_final: 0.7868 (ppp)
REVERT: B  660 CYS cc_start: 0.8705 (m) cc_final: 0.8244 (m)
REVERT: B  677 TYR cc_start: 0.8719 (m-80) cc_final: 0.7941 (m-80)
REVERT: B  704 CYS cc_start: 0.8164 (p) cc_final: 0.7927 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.1587
  time to fit residues: 41.5303
Evaluate side-chains
  147 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 497 HIS
A 681 HIS
A 755 HIS
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 HIS
B 499 ASN
B 681 HIS
B 755 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.094269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.075142 restraints weight = 19767.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.077750 restraints weight = 12765.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.079663 restraints weight = 9317.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6594  Z= 0.186
  Angle     :  0.637   7.146   8928  Z= 0.332
  Chirality :  0.043   0.143   1046
  Planarity :  0.004   0.045   1170
  Dihedral  :  4.465  15.401    918
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 14.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  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: -2.08 (0.28), residues: 856
  helix:  0.38 (0.27), residues: 372
  sheet: -2.46 (0.41), residues: 146
  loop : -2.90 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 768 
 HIS   0.010   0.001   HIS B 559 
 PHE   0.012   0.002   PHE A 387 
 TYR   0.018   0.001   TYR B 654 
 ARG   0.005   0.000   ARG A 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03298 (  290)
  hydrogen bonds       : angle       4.74276 (  840)
  covalent geometry    : bond        0.00405 ( 6594)
  covalent geometry    : angle       0.63739 ( 8928)

*********************** 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
  166 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7658 (mm-30)
REVERT: A  481 MET cc_start: 0.8035 (mtp) cc_final: 0.7625 (mtp)
REVERT: A  488 LEU cc_start: 0.9310 (tp) cc_final: 0.9002 (tp)
REVERT: A  504 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8901 (tm-30)
REVERT: A  528 ILE cc_start: 0.9091 (tp) cc_final: 0.8808 (pt)
REVERT: A  534 MET cc_start: 0.8699 (tpp) cc_final: 0.8280 (tpp)
REVERT: A  571 HIS cc_start: 0.8469 (m90) cc_final: 0.8168 (m90)
REVERT: A  574 ILE cc_start: 0.9611 (mt) cc_final: 0.9201 (tp)
REVERT: A  575 ASP cc_start: 0.8884 (t0) cc_final: 0.8577 (t0)
REVERT: A  654 TYR cc_start: 0.7522 (m-10) cc_final: 0.7234 (m-10)
REVERT: A  660 CYS cc_start: 0.8496 (m) cc_final: 0.8057 (m)
REVERT: A  677 TYR cc_start: 0.8733 (m-80) cc_final: 0.8040 (m-80)
REVERT: B  353 GLU cc_start: 0.8700 (mp0) cc_final: 0.8399 (mp0)
REVERT: B  389 LEU cc_start: 0.8978 (mm) cc_final: 0.8535 (pp)
REVERT: B  481 MET cc_start: 0.8225 (mtp) cc_final: 0.7724 (mtp)
REVERT: B  488 LEU cc_start: 0.9169 (tp) cc_final: 0.8842 (tp)
REVERT: B  534 MET cc_start: 0.8710 (tpp) cc_final: 0.8048 (tpp)
REVERT: B  536 ASN cc_start: 0.9020 (t0) cc_final: 0.8772 (m-40)
REVERT: B  537 HIS cc_start: 0.8642 (m90) cc_final: 0.8331 (m90)
REVERT: B  551 ARG cc_start: 0.9485 (mmm-85) cc_final: 0.9281 (mmm-85)
REVERT: B  558 LEU cc_start: 0.9154 (mt) cc_final: 0.8797 (mt)
REVERT: B  571 HIS cc_start: 0.8520 (m90) cc_final: 0.8212 (m90)
REVERT: B  575 ASP cc_start: 0.8915 (t0) cc_final: 0.8444 (t0)
REVERT: B  660 CYS cc_start: 0.8540 (m) cc_final: 0.8313 (m)
REVERT: B  677 TYR cc_start: 0.8739 (m-80) cc_final: 0.8033 (m-80)
REVERT: B  704 CYS cc_start: 0.8313 (p) cc_final: 0.8105 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1522
  time to fit residues: 34.7510
Evaluate side-chains
  135 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 85 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 81 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0980
   chunk 59 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 497 HIS
A 499 ASN
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 HIS
B 559 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.094422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.075158 restraints weight = 19954.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.077752 restraints weight = 13038.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.079650 restraints weight = 9588.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6594  Z= 0.159
  Angle     :  0.618   6.104   8928  Z= 0.322
  Chirality :  0.044   0.157   1046
  Planarity :  0.004   0.045   1170
  Dihedral  :  4.478  15.348    918
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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: -1.89 (0.29), residues: 856
  helix:  0.42 (0.27), residues: 372
  sheet: -2.05 (0.43), residues: 134
  loop : -2.82 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 768 
 HIS   0.005   0.001   HIS B 559 
 PHE   0.021   0.002   PHE B 616 
 TYR   0.009   0.001   TYR B 654 
 ARG   0.004   0.000   ARG A 731 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03272 (  290)
  hydrogen bonds       : angle       4.67996 (  840)
  covalent geometry    : bond        0.00352 ( 6594)
  covalent geometry    : angle       0.61751 ( 8928)

*********************** 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
  168 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7657 (mm-30)
REVERT: A  481 MET cc_start: 0.8008 (mtp) cc_final: 0.7575 (mtp)
REVERT: A  488 LEU cc_start: 0.9307 (tp) cc_final: 0.8994 (tp)
REVERT: A  504 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8895 (tm-30)
REVERT: A  534 MET cc_start: 0.8684 (tpp) cc_final: 0.8189 (tpp)
REVERT: A  571 HIS cc_start: 0.8397 (m90) cc_final: 0.8096 (m90)
REVERT: A  575 ASP cc_start: 0.8951 (t0) cc_final: 0.8667 (t0)
REVERT: A  660 CYS cc_start: 0.8455 (m) cc_final: 0.7931 (m)
REVERT: A  677 TYR cc_start: 0.8692 (m-80) cc_final: 0.8053 (m-80)
REVERT: B  353 GLU cc_start: 0.8712 (mp0) cc_final: 0.8328 (mp0)
REVERT: B  481 MET cc_start: 0.8155 (mtp) cc_final: 0.7691 (mtp)
REVERT: B  488 LEU cc_start: 0.9192 (tp) cc_final: 0.8861 (tp)
REVERT: B  504 GLU cc_start: 0.9243 (pp20) cc_final: 0.9002 (pp20)
REVERT: B  534 MET cc_start: 0.8750 (tpp) cc_final: 0.8340 (tpp)
REVERT: B  551 ARG cc_start: 0.9459 (mmm-85) cc_final: 0.9256 (mmm-85)
REVERT: B  558 LEU cc_start: 0.9162 (mt) cc_final: 0.8824 (mt)
REVERT: B  571 HIS cc_start: 0.8489 (m90) cc_final: 0.8161 (m90)
REVERT: B  575 ASP cc_start: 0.8979 (t0) cc_final: 0.8530 (t0)
REVERT: B  660 CYS cc_start: 0.8584 (m) cc_final: 0.8354 (m)
REVERT: B  677 TYR cc_start: 0.8767 (m-80) cc_final: 0.8064 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1596
  time to fit residues: 36.4667
Evaluate side-chains
  127 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 69 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 83 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 497 HIS
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.092371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.073657 restraints weight = 20177.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.076212 restraints weight = 13023.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.078114 restraints weight = 9510.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.4275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6594  Z= 0.214
  Angle     :  0.676   9.063   8928  Z= 0.351
  Chirality :  0.045   0.157   1046
  Planarity :  0.004   0.043   1170
  Dihedral  :  4.731  16.489    918
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  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: -1.97 (0.29), residues: 856
  helix:  0.34 (0.28), residues: 372
  sheet: -2.09 (0.42), residues: 134
  loop : -2.84 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 768 
 HIS   0.004   0.001   HIS B 559 
 PHE   0.021   0.002   PHE A 616 
 TYR   0.015   0.002   TYR B 654 
 ARG   0.003   0.000   ARG A 731 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03630 (  290)
  hydrogen bonds       : angle       4.82938 (  840)
  covalent geometry    : bond        0.00467 ( 6594)
  covalent geometry    : angle       0.67586 ( 8928)

*********************** 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
  161 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7776 (mm-30)
REVERT: A  481 MET cc_start: 0.7998 (mtp) cc_final: 0.7585 (mtp)
REVERT: A  488 LEU cc_start: 0.9222 (tp) cc_final: 0.8945 (tp)
REVERT: A  504 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8931 (tm-30)
REVERT: A  534 MET cc_start: 0.8823 (tpp) cc_final: 0.8372 (tpp)
REVERT: A  567 GLU cc_start: 0.7169 (mp0) cc_final: 0.6682 (mp0)
REVERT: A  571 HIS cc_start: 0.8430 (m90) cc_final: 0.8156 (m90)
REVERT: A  575 ASP cc_start: 0.9027 (t0) cc_final: 0.8726 (t0)
REVERT: A  660 CYS cc_start: 0.8529 (m) cc_final: 0.8005 (m)
REVERT: A  669 GLU cc_start: 0.8822 (tt0) cc_final: 0.8608 (tt0)
REVERT: A  677 TYR cc_start: 0.8768 (m-80) cc_final: 0.8053 (m-80)
REVERT: A  704 CYS cc_start: 0.8311 (p) cc_final: 0.8093 (p)
REVERT: B  389 LEU cc_start: 0.9020 (mm) cc_final: 0.8562 (pp)
REVERT: B  481 MET cc_start: 0.8107 (mtp) cc_final: 0.7637 (mtp)
REVERT: B  488 LEU cc_start: 0.9179 (tp) cc_final: 0.8885 (tp)
REVERT: B  534 MET cc_start: 0.8762 (tpp) cc_final: 0.8262 (tpp)
REVERT: B  571 HIS cc_start: 0.8505 (m90) cc_final: 0.8207 (m90)
REVERT: B  575 ASP cc_start: 0.9049 (t0) cc_final: 0.8610 (t0)
REVERT: B  601 MET cc_start: 0.8562 (ppp) cc_final: 0.7437 (tmm)
REVERT: B  660 CYS cc_start: 0.8717 (m) cc_final: 0.8491 (m)
REVERT: B  677 TYR cc_start: 0.8780 (m-80) cc_final: 0.8065 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1784
  time to fit residues: 39.7115
Evaluate side-chains
  130 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 82 optimal weight:    0.4980
   chunk 5 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 497 HIS
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.096637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.077208 restraints weight = 19831.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.079986 restraints weight = 12693.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.082045 restraints weight = 9173.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6594  Z= 0.124
  Angle     :  0.629   5.949   8928  Z= 0.325
  Chirality :  0.044   0.149   1046
  Planarity :  0.004   0.042   1170
  Dihedral  :  4.412  14.817    918
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    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: -1.74 (0.29), residues: 856
  helix:  0.58 (0.28), residues: 360
  sheet: -2.07 (0.43), residues: 134
  loop : -2.63 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 748 
 HIS   0.003   0.001   HIS B 559 
 PHE   0.025   0.002   PHE B 616 
 TYR   0.008   0.001   TYR A 654 
 ARG   0.005   0.000   ARG A 731 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03269 (  290)
  hydrogen bonds       : angle       4.67618 (  840)
  covalent geometry    : bond        0.00277 ( 6594)
  covalent geometry    : angle       0.62933 ( 8928)

*********************** 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
  168 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 LEU cc_start: 0.9312 (pp) cc_final: 0.9071 (mm)
REVERT: A  451 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7337 (mm-30)
REVERT: A  481 MET cc_start: 0.7977 (mtp) cc_final: 0.7699 (mtp)
REVERT: A  488 LEU cc_start: 0.9099 (tp) cc_final: 0.8847 (tp)
REVERT: A  504 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8816 (tm-30)
REVERT: A  534 MET cc_start: 0.8780 (tpp) cc_final: 0.8257 (tpp)
REVERT: A  537 HIS cc_start: 0.8711 (m90) cc_final: 0.8477 (m90)
REVERT: A  567 GLU cc_start: 0.6892 (mp0) cc_final: 0.6647 (mp0)
REVERT: A  571 HIS cc_start: 0.8447 (m90) cc_final: 0.8211 (m90)
REVERT: A  660 CYS cc_start: 0.8370 (m) cc_final: 0.7704 (m)
REVERT: A  677 TYR cc_start: 0.8630 (m-80) cc_final: 0.8021 (m-80)
REVERT: B  389 LEU cc_start: 0.8982 (mm) cc_final: 0.8512 (pp)
REVERT: B  481 MET cc_start: 0.8069 (mtp) cc_final: 0.7685 (mtp)
REVERT: B  488 LEU cc_start: 0.9091 (tp) cc_final: 0.8797 (tp)
REVERT: B  504 GLU cc_start: 0.9121 (pp20) cc_final: 0.8784 (pp20)
REVERT: B  534 MET cc_start: 0.8746 (tpp) cc_final: 0.8066 (tpp)
REVERT: B  571 HIS cc_start: 0.8429 (m90) cc_final: 0.8146 (m90)
REVERT: B  575 ASP cc_start: 0.8928 (t0) cc_final: 0.8561 (t0)
REVERT: B  601 MET cc_start: 0.8467 (ppp) cc_final: 0.7281 (tmm)
REVERT: B  651 LYS cc_start: 0.9506 (mttm) cc_final: 0.9071 (mptt)
REVERT: B  660 CYS cc_start: 0.8512 (m) cc_final: 0.8236 (m)
REVERT: B  677 TYR cc_start: 0.8734 (m-80) cc_final: 0.8115 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2057
  time to fit residues: 47.6664
Evaluate side-chains
  133 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 58 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 497 HIS
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.097286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.077822 restraints weight = 19773.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.080586 restraints weight = 12735.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.082678 restraints weight = 9256.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6594  Z= 0.116
  Angle     :  0.627   7.898   8928  Z= 0.319
  Chirality :  0.043   0.153   1046
  Planarity :  0.004   0.042   1170
  Dihedral  :  4.251  15.777    918
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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: -1.69 (0.29), residues: 856
  helix:  0.54 (0.28), residues: 360
  sheet: -2.00 (0.43), residues: 134
  loop : -2.53 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 748 
 HIS   0.003   0.001   HIS A 497 
 PHE   0.025   0.002   PHE A 616 
 TYR   0.008   0.001   TYR A 654 
 ARG   0.005   0.000   ARG A 731 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03088 (  290)
  hydrogen bonds       : angle       4.54842 (  840)
  covalent geometry    : bond        0.00262 ( 6594)
  covalent geometry    : angle       0.62650 ( 8928)

********************** 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
  175 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7603 (mp0)
REVERT: A  389 LEU cc_start: 0.9333 (pp) cc_final: 0.9059 (mm)
REVERT: A  481 MET cc_start: 0.8035 (mtp) cc_final: 0.7776 (mtp)
REVERT: A  488 LEU cc_start: 0.9046 (tp) cc_final: 0.8799 (tp)
REVERT: A  504 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8828 (tm-30)
REVERT: A  534 MET cc_start: 0.8664 (tpp) cc_final: 0.8200 (tpp)
REVERT: A  558 LEU cc_start: 0.8992 (mt) cc_final: 0.8756 (mp)
REVERT: A  571 HIS cc_start: 0.8497 (m90) cc_final: 0.8266 (m90)
REVERT: A  660 CYS cc_start: 0.8367 (m) cc_final: 0.7763 (m)
REVERT: A  677 TYR cc_start: 0.8620 (m-80) cc_final: 0.8058 (m-80)
REVERT: A  750 LEU cc_start: 0.9107 (tt) cc_final: 0.8832 (tp)
REVERT: B  389 LEU cc_start: 0.8955 (mm) cc_final: 0.8472 (pp)
REVERT: B  481 MET cc_start: 0.7870 (mtp) cc_final: 0.7577 (mtp)
REVERT: B  488 LEU cc_start: 0.8952 (tp) cc_final: 0.8634 (tp)
REVERT: B  504 GLU cc_start: 0.9108 (pp20) cc_final: 0.8730 (pp20)
REVERT: B  534 MET cc_start: 0.8750 (tpp) cc_final: 0.8539 (tpp)
REVERT: B  558 LEU cc_start: 0.9204 (mt) cc_final: 0.8945 (tt)
REVERT: B  567 GLU cc_start: 0.6980 (mp0) cc_final: 0.6453 (mp0)
REVERT: B  571 HIS cc_start: 0.8446 (m90) cc_final: 0.8119 (m90)
REVERT: B  575 ASP cc_start: 0.8898 (t0) cc_final: 0.8536 (t0)
REVERT: B  601 MET cc_start: 0.8331 (ppp) cc_final: 0.7149 (tmm)
REVERT: B  651 LYS cc_start: 0.9506 (mttm) cc_final: 0.9082 (mptt)
REVERT: B  660 CYS cc_start: 0.8545 (m) cc_final: 0.8231 (m)
REVERT: B  677 TYR cc_start: 0.8732 (m-80) cc_final: 0.8114 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1709
  time to fit residues: 41.1579
Evaluate side-chains
  134 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0670
   chunk 9 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.1722

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

Flipped N/Q/H residues before XYZ refinement:
A 497 HIS
A 556 GLN
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.095885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.076452 restraints weight = 20097.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.079208 restraints weight = 12776.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.081259 restraints weight = 9197.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.4855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6594  Z= 0.125
  Angle     :  0.635   7.881   8928  Z= 0.325
  Chirality :  0.043   0.147   1046
  Planarity :  0.004   0.041   1170
  Dihedral  :  4.232  15.239    918
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.14 %
    Favored  : 99.71 %
  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 (0.29), residues: 856
  helix:  0.57 (0.28), residues: 360
  sheet: -1.98 (0.43), residues: 134
  loop : -2.48 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 748 
 HIS   0.005   0.001   HIS B 559 
 PHE   0.025   0.002   PHE B 616 
 TYR   0.007   0.001   TYR B 654 
 ARG   0.005   0.000   ARG A 731 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03060 (  290)
  hydrogen bonds       : angle       4.54929 (  840)
  covalent geometry    : bond        0.00282 ( 6594)
  covalent geometry    : angle       0.63541 ( 8928)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2224.55 seconds
wall clock time: 39 minutes 55.64 seconds (2395.64 seconds total)