Starting phenix.real_space_refine
on Tue Feb 11 20:09:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wxh_32879/02_2025/7wxh_32879.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wxh_32879/02_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_32879/02_2025/7wxh_32879.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wxh_32879/02_2025/7wxh_32879.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wxh_32879/02_2025/7wxh_32879.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wxh_32879/02_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-5592/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: 5.63, per 1000 atoms: 0.87
  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: 1.66
  Conformation dependent library (CDL) restraints added in 933.7 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: 0.83
  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: 1.96

  Time building geometry restraints manager: 1.91 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:             1.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.750
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.650
-------------------------------------------------------------------------------
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= 0.412
  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 

*********************** 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  : 0.798 
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: 0.2244
  time to fit residues: 58.7091
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  : 0.755 
-------------------------------------------------------------------------------
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 = 0.072505 restraints weight = 19868.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.075031 restraints weight = 12938.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.076916 restraints weight = 9554.987|
|-----------------------------------------------------------------------------|
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= 0.242
  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 

*********************** 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  : 0.765 
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: 0.8120 (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: 0.8824 (m-80) cc_final: 0.8156 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1732
  time to fit residues: 43.9735
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  : 0.730 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 60 optimal weight:    9.9990
   chunk 59 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0050
   chunk 65 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.2998

-------------------------------------------------------------------------------
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 = 0.3523 r_free = 0.3523 target = 0.095122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.075151 restraints weight = 19408.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.077826 restraints weight = 12468.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.079745 restraints weight = 9112.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3015

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= 0.193
  Angle     :  0.611   5.712   8928  Z= 0.321
  Chirality :  0.043   0.144   1046
  Planarity :  0.004   0.042   1170
  Dihedral  :  4.697  15.813    918
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  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: -2.39 (0.28), residues: 856
  helix:  0.22 (0.27), residues: 358
  sheet: -2.28 (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   0.015   0.002   PHE B 387 
 TYR   0.006   0.001   TYR A 654 
 ARG   0.004   0.000   ARG A 718 

*********************** 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
  185 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 PHE cc_start: 0.9003 (t80) cc_final: 0.8469 (t80)
REVERT: A  481 MET cc_start: 0.8003 (mtp) cc_final: 0.7552 (mtp)
REVERT: A  488 LEU cc_start: 0.9349 (tp) cc_final: 0.9121 (tp)
REVERT: A  534 MET cc_start: 0.8772 (tpp) cc_final: 0.8269 (tpp)
REVERT: A  571 HIS cc_start: 0.8397 (m90) cc_final: 0.8060 (m90)
REVERT: A  574 ILE cc_start: 0.9579 (mt) cc_final: 0.9139 (tp)
REVERT: A  575 ASP cc_start: 0.9028 (t0) cc_final: 0.8621 (t0)
REVERT: A  601 MET cc_start: 0.7883 (tmm) cc_final: 0.7273 (tmm)
REVERT: A  654 TYR cc_start: 0.7875 (m-10) cc_final: 0.7509 (m-10)
REVERT: A  677 TYR cc_start: 0.8746 (m-80) cc_final: 0.8064 (m-80)
REVERT: B  363 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8782 (tp40)
REVERT: B  389 LEU cc_start: 0.8843 (mp) cc_final: 0.8416 (pp)
REVERT: B  451 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7421 (pm20)
REVERT: B  481 MET cc_start: 0.8120 (mtp) cc_final: 0.7656 (mtp)
REVERT: B  488 LEU cc_start: 0.9162 (tp) cc_final: 0.8885 (tp)
REVERT: B  504 GLU cc_start: 0.9567 (pt0) cc_final: 0.9335 (pp20)
REVERT: B  534 MET cc_start: 0.8635 (tpp) cc_final: 0.7952 (tpp)
REVERT: B  537 HIS cc_start: 0.8845 (m90) cc_final: 0.8575 (m90)
REVERT: B  558 LEU cc_start: 0.9195 (mt) cc_final: 0.8747 (mt)
REVERT: B  571 HIS cc_start: 0.8565 (m90) cc_final: 0.8295 (m90)
REVERT: B  575 ASP cc_start: 0.8969 (t0) cc_final: 0.8474 (t0)
REVERT: B  582 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8757 (mmmt)
REVERT: B  654 TYR cc_start: 0.7943 (m-80) cc_final: 0.7677 (m-10)
REVERT: B  677 TYR cc_start: 0.8834 (m-80) cc_final: 0.8127 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1700
  time to fit residues: 42.7123
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  : 0.698 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 69 optimal weight:    9.9990
   chunk 56 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 76 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   overall best weight:    1.9384

-------------------------------------------------------------------------------
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
B 652 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.093698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.073836 restraints weight = 19955.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.076495 restraints weight = 12931.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.078395 restraints weight = 9500.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6594  Z= 0.229
  Angle     :  0.610   5.796   8928  Z= 0.317
  Chirality :  0.043   0.154   1046
  Planarity :  0.004   0.046   1170
  Dihedral  :  4.599  15.915    918
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  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:  0.47 (0.27), residues: 360
  sheet: -2.21 (0.44), residues: 136
  loop : -3.04 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 768 
 HIS   0.003   0.001   HIS A 497 
 PHE   0.008   0.002   PHE B 760 
 TYR   0.007   0.001   TYR A 654 
 ARG   0.003   0.000   ARG A 718 

*********************** 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
  172 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.755 
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: 0.9412 (pp) cc_final: 0.9127 (mm)
REVERT: A  481 MET cc_start: 0.7993 (mtp) cc_final: 0.7620 (mtp)
REVERT: A  488 LEU cc_start: 0.9291 (tp) cc_final: 0.8980 (tp)
REVERT: A  528 ILE cc_start: 0.9149 (tp) cc_final: 0.8867 (pt)
REVERT: A  534 MET cc_start: 0.8806 (tpp) cc_final: 0.8299 (tpp)
REVERT: A  571 HIS cc_start: 0.8474 (m90) cc_final: 0.8139 (m90)
REVERT: A  574 ILE cc_start: 0.9646 (mt) cc_final: 0.9186 (tp)
REVERT: A  575 ASP cc_start: 0.8949 (t0) cc_final: 0.8566 (t0)
REVERT: A  601 MET cc_start: 0.8117 (tmm) cc_final: 0.7280 (tmm)
REVERT: A  677 TYR cc_start: 0.8716 (m-80) cc_final: 0.8093 (m-80)
REVERT: B  363 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8304 (tp40)
REVERT: B  389 LEU cc_start: 0.9035 (mp) cc_final: 0.8697 (pp)
REVERT: B  481 MET cc_start: 0.8134 (mtp) cc_final: 0.7691 (mtp)
REVERT: B  488 LEU cc_start: 0.9125 (tp) cc_final: 0.8807 (tp)
REVERT: B  504 GLU cc_start: 0.9565 (pt0) cc_final: 0.9274 (pp20)
REVERT: B  551 ARG cc_start: 0.9512 (mmm-85) cc_final: 0.9292 (mmm-85)
REVERT: B  558 LEU cc_start: 0.9208 (mt) cc_final: 0.8778 (mt)
REVERT: B  571 HIS cc_start: 0.8519 (m90) cc_final: 0.8225 (m90)
REVERT: B  575 ASP cc_start: 0.8893 (t0) cc_final: 0.8382 (t0)
REVERT: B  677 TYR cc_start: 0.8772 (m-80) cc_final: 0.8013 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1669
  time to fit residues: 38.8332
Evaluate side-chains
  139 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0270
   chunk 34 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 37 optimal weight:    0.4980
   chunk 60 optimal weight:    0.0370
   overall best weight:    0.3716

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.097935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.078522 restraints weight = 19354.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.081222 restraints weight = 12639.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.083159 restraints weight = 9229.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6594  Z= 0.154
  Angle     :  0.601   7.505   8928  Z= 0.310
  Chirality :  0.043   0.146   1046
  Planarity :  0.004   0.042   1170
  Dihedral  :  4.302  15.718    918
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  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: -1.75 (0.29), residues: 856
  helix:  0.76 (0.28), residues: 350
  sheet: -1.93 (0.44), residues: 132
  loop : -2.83 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 748 
 HIS   0.003   0.000   HIS B 497 
 PHE   0.006   0.001   PHE B 719 
 TYR   0.007   0.001   TYR B 654 
 ARG   0.010   0.000   ARG A 370 

*********************** 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
  191 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 LEU cc_start: 0.9326 (pp) cc_final: 0.9027 (mm)
REVERT: A  451 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7531 (mm-30)
REVERT: A  528 ILE cc_start: 0.9022 (tp) cc_final: 0.8788 (pt)
REVERT: A  534 MET cc_start: 0.8707 (tpp) cc_final: 0.8353 (tpp)
REVERT: A  571 HIS cc_start: 0.8356 (m90) cc_final: 0.8047 (m90)
REVERT: A  574 ILE cc_start: 0.9598 (mt) cc_final: 0.9117 (tp)
REVERT: A  575 ASP cc_start: 0.8756 (t0) cc_final: 0.8524 (t0)
REVERT: A  603 THR cc_start: 0.9083 (t) cc_final: 0.8744 (t)
REVERT: A  660 CYS cc_start: 0.8523 (m) cc_final: 0.8057 (m)
REVERT: A  677 TYR cc_start: 0.8589 (m-80) cc_final: 0.7983 (m-80)
REVERT: A  704 CYS cc_start: 0.8134 (p) cc_final: 0.7916 (p)
REVERT: B  363 GLN cc_start: 0.8842 (tp-100) cc_final: 0.8583 (tp40)
REVERT: B  481 MET cc_start: 0.8156 (mtp) cc_final: 0.7835 (mtp)
REVERT: B  488 LEU cc_start: 0.9125 (tp) cc_final: 0.8857 (tp)
REVERT: B  516 GLU cc_start: 0.7146 (tt0) cc_final: 0.6930 (tt0)
REVERT: B  534 MET cc_start: 0.8863 (tpp) cc_final: 0.8542 (tpp)
REVERT: B  551 ARG cc_start: 0.9478 (mmm-85) cc_final: 0.9214 (mmm-85)
REVERT: B  571 HIS cc_start: 0.8448 (m90) cc_final: 0.8118 (m90)
REVERT: B  575 ASP cc_start: 0.8703 (t0) cc_final: 0.8200 (t0)
REVERT: B  601 MET cc_start: 0.8121 (ppp) cc_final: 0.7888 (ppp)
REVERT: B  651 LYS cc_start: 0.9418 (mttm) cc_final: 0.8870 (mmtm)
REVERT: B  660 CYS cc_start: 0.8736 (m) cc_final: 0.8401 (m)
REVERT: B  677 TYR cc_start: 0.8699 (m-80) cc_final: 0.7377 (m-80)
REVERT: B  704 CYS cc_start: 0.8136 (p) cc_final: 0.7894 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1687
  time to fit residues: 43.7429
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  : 0.838 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 681 HIS
B 755 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.092594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.073515 restraints weight = 19803.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.076122 restraints weight = 12696.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.078056 restraints weight = 9215.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.3904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6594  Z= 0.320
  Angle     :  0.670   7.127   8928  Z= 0.348
  Chirality :  0.044   0.145   1046
  Planarity :  0.004   0.045   1170
  Dihedral  :  4.654  16.127    918
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.46 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  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: -2.26 (0.28), residues: 856
  helix:  0.21 (0.27), residues: 372
  sheet: -2.56 (0.40), residues: 146
  loop : -2.96 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 768 
 HIS   0.006   0.001   HIS B 652 
 PHE   0.011   0.002   PHE A 387 
 TYR   0.022   0.002   TYR B 654 
 ARG   0.004   0.001   ARG A 360 

*********************** 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
  168 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.729 
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: 0.8054 (mm-30) cc_final: 0.7705 (mm-30)
REVERT: A  488 LEU cc_start: 0.9095 (tp) cc_final: 0.8817 (tp)
REVERT: A  504 GLU cc_start: 0.9308 (pp20) cc_final: 0.9054 (pp20)
REVERT: A  528 ILE cc_start: 0.9121 (tp) cc_final: 0.8825 (pt)
REVERT: A  571 HIS cc_start: 0.8444 (m90) cc_final: 0.8120 (m90)
REVERT: A  575 ASP cc_start: 0.8940 (t0) cc_final: 0.8578 (t0)
REVERT: A  601 MET cc_start: 0.8377 (ptm) cc_final: 0.8082 (ptm)
REVERT: A  660 CYS cc_start: 0.8461 (m) cc_final: 0.8166 (m)
REVERT: A  677 TYR cc_start: 0.8765 (m-80) cc_final: 0.8037 (m-80)
REVERT: B  353 GLU cc_start: 0.8672 (mp0) cc_final: 0.8419 (mp0)
REVERT: B  389 LEU cc_start: 0.8952 (mm) cc_final: 0.8480 (pp)
REVERT: B  481 MET cc_start: 0.8218 (mtp) cc_final: 0.7703 (mtp)
REVERT: B  488 LEU cc_start: 0.9066 (tp) cc_final: 0.8715 (tp)
REVERT: B  504 GLU cc_start: 0.9233 (pp20) cc_final: 0.8988 (pp20)
REVERT: B  575 ASP cc_start: 0.9001 (t0) cc_final: 0.8486 (t0)
REVERT: B  601 MET cc_start: 0.8538 (ppp) cc_final: 0.7631 (tmm)
REVERT: B  651 LYS cc_start: 0.9457 (mttm) cc_final: 0.8878 (mmtm)
REVERT: B  660 CYS cc_start: 0.8605 (m) cc_final: 0.8377 (m)
REVERT: B  677 TYR cc_start: 0.8767 (m-80) cc_final: 0.7427 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1634
  time to fit residues: 37.3683
Evaluate side-chains
  139 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 48 optimal weight:    9.9990
   chunk 85 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 23 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 499 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.096258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.076889 restraints weight = 19560.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.079561 restraints weight = 12638.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.081546 restraints weight = 9214.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6594  Z= 0.185
  Angle     :  0.631   8.097   8928  Z= 0.329
  Chirality :  0.044   0.163   1046
  Planarity :  0.004   0.045   1170
  Dihedral  :  4.430  15.424    918
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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: -1.86 (0.29), residues: 856
  helix:  0.50 (0.28), residues: 360
  sheet: -2.07 (0.43), residues: 134
  loop : -2.74 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 748 
 HIS   0.004   0.001   HIS A 497 
 PHE   0.023   0.002   PHE A 616 
 TYR   0.006   0.001   TYR A 654 
 ARG   0.006   0.000   ARG B 551 

*********************** 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
  166 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 LEU cc_start: 0.9361 (pp) cc_final: 0.9106 (mm)
REVERT: A  451 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7636 (mm-30)
REVERT: A  488 LEU cc_start: 0.9072 (tp) cc_final: 0.8786 (tp)
REVERT: A  534 MET cc_start: 0.8740 (tpp) cc_final: 0.8389 (tpp)
REVERT: A  571 HIS cc_start: 0.8423 (m90) cc_final: 0.8134 (m90)
REVERT: A  575 ASP cc_start: 0.8848 (t0) cc_final: 0.8586 (t0)
REVERT: A  601 MET cc_start: 0.8306 (ptm) cc_final: 0.8030 (ptm)
REVERT: A  660 CYS cc_start: 0.8377 (m) cc_final: 0.8031 (m)
REVERT: A  677 TYR cc_start: 0.8675 (m-80) cc_final: 0.8060 (m-80)
REVERT: B  481 MET cc_start: 0.8148 (mtp) cc_final: 0.7709 (mtp)
REVERT: B  488 LEU cc_start: 0.9166 (tp) cc_final: 0.8809 (tp)
REVERT: B  534 MET cc_start: 0.8678 (tpp) cc_final: 0.8421 (tpp)
REVERT: B  537 HIS cc_start: 0.8704 (m90) cc_final: 0.8486 (m170)
REVERT: B  558 LEU cc_start: 0.9219 (mt) cc_final: 0.8891 (mt)
REVERT: B  571 HIS cc_start: 0.8503 (m90) cc_final: 0.8209 (m90)
REVERT: B  575 ASP cc_start: 0.8880 (t0) cc_final: 0.8395 (t0)
REVERT: B  601 MET cc_start: 0.8533 (ppp) cc_final: 0.7591 (tmm)
REVERT: B  651 LYS cc_start: 0.9455 (mttm) cc_final: 0.9108 (mptt)
REVERT: B  660 CYS cc_start: 0.8562 (m) cc_final: 0.8203 (m)
REVERT: B  677 TYR cc_start: 0.8752 (m-80) cc_final: 0.8069 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1627
  time to fit residues: 36.8844
Evaluate side-chains
  131 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   chunk 7 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0370
   chunk 36 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    2.1864

-------------------------------------------------------------------------------
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
B 536 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.094728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.076328 restraints weight = 19863.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.078934 restraints weight = 12765.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.080862 restraints weight = 9260.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6594  Z= 0.259
  Angle     :  0.657   7.130   8928  Z= 0.345
  Chirality :  0.044   0.151   1046
  Planarity :  0.004   0.046   1170
  Dihedral  :  4.516  15.429    918
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.72 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.29), residues: 856
  helix:  0.39 (0.28), residues: 360
  sheet: -2.11 (0.42), residues: 134
  loop : -2.71 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 748 
 HIS   0.005   0.001   HIS A 497 
 PHE   0.011   0.002   PHE A 713 
 TYR   0.011   0.001   TYR B 654 
 ARG   0.005   0.000   ARG B 551 

*********************** 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
  160 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 LEU cc_start: 0.9310 (pp) cc_final: 0.9060 (mm)
REVERT: A  451 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7672 (mm-30)
REVERT: A  481 MET cc_start: 0.8155 (mtp) cc_final: 0.7744 (mtp)
REVERT: A  488 LEU cc_start: 0.8992 (tp) cc_final: 0.8746 (tp)
REVERT: A  534 MET cc_start: 0.8707 (tpp) cc_final: 0.8213 (tpp)
REVERT: A  537 HIS cc_start: 0.8808 (m90) cc_final: 0.8604 (m90)
REVERT: A  571 HIS cc_start: 0.8379 (m90) cc_final: 0.8080 (m90)
REVERT: A  575 ASP cc_start: 0.8880 (t0) cc_final: 0.8530 (t0)
REVERT: A  601 MET cc_start: 0.8279 (ptm) cc_final: 0.8030 (ptm)
REVERT: A  654 TYR cc_start: 0.7494 (m-10) cc_final: 0.7107 (m-10)
REVERT: A  660 CYS cc_start: 0.8419 (m) cc_final: 0.8068 (m)
REVERT: A  677 TYR cc_start: 0.8667 (m-80) cc_final: 0.8031 (m-80)
REVERT: B  481 MET cc_start: 0.8089 (mtp) cc_final: 0.7614 (mtp)
REVERT: B  488 LEU cc_start: 0.9129 (tp) cc_final: 0.8784 (tp)
REVERT: B  534 MET cc_start: 0.8696 (tpp) cc_final: 0.7962 (tpp)
REVERT: B  571 HIS cc_start: 0.8502 (m90) cc_final: 0.8201 (m90)
REVERT: B  575 ASP cc_start: 0.8944 (t0) cc_final: 0.8516 (t0)
REVERT: B  601 MET cc_start: 0.8642 (ppp) cc_final: 0.7711 (tmm)
REVERT: B  660 CYS cc_start: 0.8520 (m) cc_final: 0.8279 (m)
REVERT: B  677 TYR cc_start: 0.8757 (m-80) cc_final: 0.8036 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1549
  time to fit residues: 34.0045
Evaluate side-chains
  125 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0970
   chunk 20 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.096373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.077182 restraints weight = 20102.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.079897 restraints weight = 12976.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.081864 restraints weight = 9434.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.4563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6594  Z= 0.188
  Angle     :  0.647   8.417   8928  Z= 0.338
  Chirality :  0.044   0.149   1046
  Planarity :  0.004   0.046   1170
  Dihedral  :  4.346  14.620    918
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    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: -1.84 (0.29), residues: 856
  helix:  0.43 (0.28), residues: 360
  sheet: -2.05 (0.43), residues: 134
  loop : -2.63 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 748 
 HIS   0.003   0.001   HIS B 497 
 PHE   0.025   0.002   PHE B 616 
 TYR   0.006   0.001   TYR A 654 
 ARG   0.005   0.000   ARG A 731 

*********************** 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
  158 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.783 
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: 0.9280 (pp) cc_final: 0.9058 (mm)
REVERT: A  451 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7298 (mm-30)
REVERT: A  481 MET cc_start: 0.8116 (mtp) cc_final: 0.7736 (mtp)
REVERT: A  488 LEU cc_start: 0.9000 (tp) cc_final: 0.8742 (tp)
REVERT: A  534 MET cc_start: 0.8671 (tpp) cc_final: 0.8165 (tpp)
REVERT: A  571 HIS cc_start: 0.8356 (m90) cc_final: 0.8086 (m90)
REVERT: A  601 MET cc_start: 0.8135 (ptm) cc_final: 0.7635 (ptm)
REVERT: A  660 CYS cc_start: 0.8373 (m) cc_final: 0.7996 (m)
REVERT: A  677 TYR cc_start: 0.8541 (m-80) cc_final: 0.8025 (m-80)
REVERT: B  481 MET cc_start: 0.7917 (mtp) cc_final: 0.7644 (mtp)
REVERT: B  488 LEU cc_start: 0.9156 (tp) cc_final: 0.8853 (tp)
REVERT: B  571 HIS cc_start: 0.8457 (m90) cc_final: 0.8204 (m90)
REVERT: B  575 ASP cc_start: 0.8812 (t0) cc_final: 0.8462 (t0)
REVERT: B  601 MET cc_start: 0.8549 (ppp) cc_final: 0.7614 (tmm)
REVERT: B  622 MET cc_start: 0.9129 (tpp) cc_final: 0.8929 (tpt)
REVERT: B  660 CYS cc_start: 0.8515 (m) cc_final: 0.8237 (m)
REVERT: B  677 TYR cc_start: 0.8626 (m-80) cc_final: 0.8002 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1526
  time to fit residues: 33.3326
Evaluate side-chains
  122 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 25 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 63 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.096913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.078076 restraints weight = 19564.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.080810 restraints weight = 12496.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.082879 restraints weight = 9002.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.4786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6594  Z= 0.190
  Angle     :  0.671   9.176   8928  Z= 0.349
  Chirality :  0.044   0.145   1046
  Planarity :  0.004   0.045   1170
  Dihedral  :  4.243  14.700    918
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.00 %
    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: -1.80 (0.29), residues: 856
  helix:  0.41 (0.28), residues: 360
  sheet: -1.98 (0.44), residues: 134
  loop : -2.57 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 748 
 HIS   0.002   0.001   HIS A 537 
 PHE   0.008   0.001   PHE A 642 
 TYR   0.006   0.001   TYR A 654 
 ARG   0.005   0.000   ARG A 731 

********************** 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
  161 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 0.803 
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: 0.9325 (pp) cc_final: 0.9088 (mm)
REVERT: A  481 MET cc_start: 0.8175 (mtp) cc_final: 0.7911 (mtp)
REVERT: A  488 LEU cc_start: 0.8968 (tp) cc_final: 0.8698 (tp)
REVERT: A  534 MET cc_start: 0.8680 (tpp) cc_final: 0.8089 (tpp)
REVERT: A  571 HIS cc_start: 0.8400 (m90) cc_final: 0.8119 (m90)
REVERT: A  601 MET cc_start: 0.8161 (ptm) cc_final: 0.7684 (ptm)
REVERT: A  660 CYS cc_start: 0.8478 (m) cc_final: 0.8188 (m)
REVERT: A  677 TYR cc_start: 0.8607 (m-80) cc_final: 0.8080 (m-80)
REVERT: A  750 LEU cc_start: 0.9142 (tt) cc_final: 0.8846 (tp)
REVERT: B  481 MET cc_start: 0.8109 (mtp) cc_final: 0.7742 (mtp)
REVERT: B  488 LEU cc_start: 0.8958 (tp) cc_final: 0.8679 (tp)
REVERT: B  571 HIS cc_start: 0.8494 (m90) cc_final: 0.8212 (m90)
REVERT: B  575 ASP cc_start: 0.8905 (t0) cc_final: 0.8488 (t0)
REVERT: B  601 MET cc_start: 0.8579 (ppp) cc_final: 0.7600 (tmm)
REVERT: B  660 CYS cc_start: 0.8504 (m) cc_final: 0.8273 (m)
REVERT: B  677 TYR cc_start: 0.8776 (m-80) cc_final: 0.8049 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1473
  time to fit residues: 33.3482
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  : 0.818 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 42 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0370
   chunk 62 optimal weight:    0.0770
   chunk 24 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 72 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0070
   overall best weight:    0.3234

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.098686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.079339 restraints weight = 19631.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.082190 restraints weight = 12448.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.084327 restraints weight = 8954.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.5014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6594  Z= 0.162
  Angle     :  0.678   8.894   8928  Z= 0.345
  Chirality :  0.044   0.143   1046
  Planarity :  0.004   0.045   1170
  Dihedral  :  4.157  17.841    918
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.58 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.29), residues: 856
  helix:  0.48 (0.28), residues: 360
  sheet: -1.85 (0.46), residues: 130
  loop : -2.40 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 748 
 HIS   0.006   0.001   HIS B 559 
 PHE   0.026   0.002   PHE B 616 
 TYR   0.005   0.001   TYR A 573 
 ARG   0.006   0.000   ARG A 731 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2061.47 seconds
wall clock time: 37 minutes 56.24 seconds (2276.24 seconds total)