Starting phenix.real_space_refine
on Tue Feb  3 19:32:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wxh_32879/02_2026/7wxh_32879.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wxh_32879/02_2026/7wxh_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wxh_32879/02_2026/7wxh_32879.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wxh_32879/02_2026/7wxh_32879.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wxh_32879/02_2026/7wxh_32879.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wxh_32879/02_2026/7wxh_32879.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 1.90, per 1000 atoms: 0.29
  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: 0.51
  Conformation dependent library (CDL) restraints added in 388.5 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: 0.16
  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: 0.80

  Time building geometry restraints manager: 0.71 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: 0.01
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:             2.630
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.090
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.990
-------------------------------------------------------------------------------
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 : 26.10
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.005   0.001   ARG B 735 
 TYR   0.009   0.001   TYR B 654 
 PHE   0.015   0.003   PHE B 706 
 TRP   0.009   0.002   TRP B 768 
 HIS   0.007   0.002   HIS B 565 

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

*********************** 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  : 0.234 
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: 0.8889 (t70) cc_final: 0.8652 (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: 0.8725 (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: 0.7552 (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: 0.9232 (mt) cc_final: 0.9020 (mt)
REVERT: B  601 MET cc_start: 0.8162 (ppp) cc_final: 0.7718 (ptt)
REVERT: B  606 ILE cc_start: 0.9494 (mp) cc_final: 0.9287 (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: 0.8349 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 208
  average time/residue: 0.0740
  time to fit residues: 19.6564
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  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 369 GLN
A 556 GLN
A 565 HIS
A 599 ASN
A 607 HIS
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 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 565 HIS
B 599 ASN
B 607 HIS
B 675 HIS
** B 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.093759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.073605 restraints weight = 19991.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.076185 restraints weight = 12923.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.078084 restraints weight = 9508.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.079444 restraints weight = 7572.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.080530 restraints weight = 6405.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6594  Z= 0.145
  Angle     :  0.651   7.000   8928  Z= 0.340
  Chirality :  0.044   0.147   1046
  Planarity :  0.004   0.042   1170
  Dihedral  :  4.989  16.407    918
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.27), residues: 856
  helix: -0.20 (0.27), residues: 346
  sheet: -2.81 (0.40), residues: 146
  loop : -3.43 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 694 
 TYR   0.005   0.001   TYR A 654 
 PHE   0.010   0.001   PHE B 760 
 TRP   0.009   0.001   TRP A 748 
 HIS   0.005   0.001   HIS A 565 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6594)
  covalent geometry    : angle       0.65072 ( 8928)
  hydrogen bonds       : bond        0.03993 (  290)
  hydrogen bonds       : angle       5.33221 (  840)

*********************** 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
  192 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.161 
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: 0.9063 (t80) cc_final: 0.8544 (t80)
REVERT: A  389 LEU cc_start: 0.9419 (pp) cc_final: 0.9198 (mp)
REVERT: A  481 MET cc_start: 0.8063 (mtp) cc_final: 0.7605 (mtp)
REVERT: A  488 LEU cc_start: 0.9362 (tp) cc_final: 0.9093 (tp)
REVERT: A  571 HIS cc_start: 0.8428 (m90) cc_final: 0.8104 (m90)
REVERT: A  574 ILE cc_start: 0.9534 (mt) cc_final: 0.9085 (tp)
REVERT: A  575 ASP cc_start: 0.9025 (t0) cc_final: 0.8648 (t0)
REVERT: A  677 TYR cc_start: 0.8715 (m-80) cc_final: 0.8115 (m-80)
REVERT: A  713 PHE cc_start: 0.8498 (m-80) cc_final: 0.8213 (m-80)
REVERT: B  363 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8441 (tp40)
REVERT: B  387 PHE cc_start: 0.8997 (t80) cc_final: 0.8692 (t80)
REVERT: B  451 GLU cc_start: 0.7863 (mm-30) cc_final: 0.6985 (pm20)
REVERT: B  481 MET cc_start: 0.8118 (mtp) cc_final: 0.7824 (mtp)
REVERT: B  488 LEU cc_start: 0.9139 (tp) cc_final: 0.8830 (tp)
REVERT: B  571 HIS cc_start: 0.8644 (m90) cc_final: 0.8376 (m90)
REVERT: B  575 ASP cc_start: 0.8936 (t0) cc_final: 0.8479 (t0)
REVERT: B  601 MET cc_start: 0.8347 (ppp) cc_final: 0.7991 (ptt)
REVERT: B  654 TYR cc_start: 0.8615 (m-80) cc_final: 0.7143 (m-10)
REVERT: B  677 TYR cc_start: 0.8791 (m-80) cc_final: 0.8007 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.0616
  time to fit residues: 16.2760
Evaluate side-chains
  152 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 29 optimal weight:    0.0570
   chunk 33 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    1.7304

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 449 GLN
A 497 HIS
A 499 ASN
B 497 HIS
B 499 ASN
B 556 GLN
B 652 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.094203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.074545 restraints weight = 19698.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.077071 restraints weight = 12916.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.078931 restraints weight = 9555.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.080318 restraints weight = 7611.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.081363 restraints weight = 6406.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2927

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= 0.150
  Angle     :  0.625   7.070   8928  Z= 0.327
  Chirality :  0.043   0.148   1046
  Planarity :  0.005   0.064   1170
  Dihedral  :  4.729  15.816    918
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.78 %
    Favored  : 95.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.28), residues: 856
  helix:  0.22 (0.27), residues: 360
  sheet: -2.34 (0.43), residues: 136
  loop : -3.25 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 694 
 TYR   0.006   0.001   TYR A 654 
 PHE   0.012   0.002   PHE A 616 
 TRP   0.006   0.001   TRP B 748 
 HIS   0.003   0.001   HIS A 707 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6594)
  covalent geometry    : angle       0.62457 ( 8928)
  hydrogen bonds       : bond        0.03602 (  290)
  hydrogen bonds       : angle       5.01595 (  840)

*********************** 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
  178 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 PHE cc_start: 0.8953 (t80) cc_final: 0.8710 (t80)
REVERT: A  481 MET cc_start: 0.7986 (mtp) cc_final: 0.7530 (mtp)
REVERT: A  488 LEU cc_start: 0.9333 (tp) cc_final: 0.9110 (tp)
REVERT: A  534 MET cc_start: 0.8747 (tpp) cc_final: 0.8364 (tpp)
REVERT: A  571 HIS cc_start: 0.8427 (m90) cc_final: 0.8105 (m90)
REVERT: A  574 ILE cc_start: 0.9590 (mt) cc_final: 0.9141 (tp)
REVERT: A  575 ASP cc_start: 0.8973 (t0) cc_final: 0.8581 (t0)
REVERT: A  601 MET cc_start: 0.7877 (tmm) cc_final: 0.7243 (tmm)
REVERT: A  654 TYR cc_start: 0.7770 (m-10) cc_final: 0.7435 (m-10)
REVERT: A  677 TYR cc_start: 0.8691 (m-80) cc_final: 0.8054 (m-80)
REVERT: A  713 PHE cc_start: 0.8419 (m-80) cc_final: 0.8167 (m-80)
REVERT: B  389 LEU cc_start: 0.8973 (mp) cc_final: 0.8530 (pp)
REVERT: B  451 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7151 (pm20)
REVERT: B  481 MET cc_start: 0.8115 (mtp) cc_final: 0.7668 (mtp)
REVERT: B  488 LEU cc_start: 0.9156 (tp) cc_final: 0.8869 (tp)
REVERT: B  534 MET cc_start: 0.8583 (tpp) cc_final: 0.7980 (tpp)
REVERT: B  537 HIS cc_start: 0.8831 (m90) cc_final: 0.8609 (m90)
REVERT: B  558 LEU cc_start: 0.9149 (mt) cc_final: 0.8702 (mt)
REVERT: B  571 HIS cc_start: 0.8568 (m90) cc_final: 0.8303 (m90)
REVERT: B  575 ASP cc_start: 0.8803 (t0) cc_final: 0.8221 (t0)
REVERT: B  582 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8645 (mmmt)
REVERT: B  654 TYR cc_start: 0.7966 (m-80) cc_final: 0.7727 (m-10)
REVERT: B  677 TYR cc_start: 0.8776 (m-80) cc_final: 0.8084 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 178
  average time/residue: 0.0558
  time to fit residues: 13.9485
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  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 36 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 57 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.095655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.075684 restraints weight = 19512.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.078378 restraints weight = 12628.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.080346 restraints weight = 9216.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.081796 restraints weight = 7270.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.082811 restraints weight = 6062.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
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   0.024   6594  Z= 0.124
  Angle     :  0.584   7.094   8928  Z= 0.305
  Chirality :  0.043   0.142   1046
  Planarity :  0.004   0.045   1170
  Dihedral  :  4.474  14.973    918
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.91 (0.29), residues: 856
  helix:  0.74 (0.28), residues: 350
  sheet: -2.19 (0.44), residues: 136
  loop : -2.98 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 694 
 TYR   0.006   0.001   TYR A 654 
 PHE   0.010   0.001   PHE B 387 
 TRP   0.007   0.001   TRP B 748 
 HIS   0.003   0.001   HIS B 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6594)
  covalent geometry    : angle       0.58411 ( 8928)
  hydrogen bonds       : bond        0.03121 (  290)
  hydrogen bonds       : angle       4.70522 (  840)

*********************** 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
  177 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.164 
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: 0.9364 (pp) cc_final: 0.9042 (mm)
REVERT: A  481 MET cc_start: 0.7922 (mtp) cc_final: 0.7566 (mtp)
REVERT: A  488 LEU cc_start: 0.9259 (tp) cc_final: 0.8963 (tp)
REVERT: A  504 GLU cc_start: 0.9054 (pp20) cc_final: 0.8646 (pp20)
REVERT: A  528 ILE cc_start: 0.9095 (tp) cc_final: 0.8832 (pt)
REVERT: A  534 MET cc_start: 0.8752 (tpp) cc_final: 0.8306 (tpp)
REVERT: A  571 HIS cc_start: 0.8480 (m90) cc_final: 0.8125 (m90)
REVERT: A  574 ILE cc_start: 0.9625 (mt) cc_final: 0.9175 (tp)
REVERT: A  575 ASP cc_start: 0.8869 (t0) cc_final: 0.8503 (t0)
REVERT: A  601 MET cc_start: 0.8003 (tmm) cc_final: 0.7212 (tmm)
REVERT: A  677 TYR cc_start: 0.8687 (m-80) cc_final: 0.8017 (m-80)
REVERT: B  389 LEU cc_start: 0.8940 (mp) cc_final: 0.8642 (pp)
REVERT: B  451 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7575 (mm-30)
REVERT: B  481 MET cc_start: 0.8152 (mtp) cc_final: 0.7685 (mtp)
REVERT: B  488 LEU cc_start: 0.9096 (tp) cc_final: 0.8763 (tp)
REVERT: B  528 ILE cc_start: 0.8982 (tp) cc_final: 0.8711 (pt)
REVERT: B  534 MET cc_start: 0.8611 (tpp) cc_final: 0.7878 (tpp)
REVERT: B  537 HIS cc_start: 0.8846 (m90) cc_final: 0.8602 (m90)
REVERT: B  551 ARG cc_start: 0.9498 (mmm-85) cc_final: 0.9242 (mmm-85)
REVERT: B  558 LEU cc_start: 0.9209 (mt) cc_final: 0.8786 (mt)
REVERT: B  571 HIS cc_start: 0.8570 (m90) cc_final: 0.8212 (m90)
REVERT: B  575 ASP cc_start: 0.8822 (t0) cc_final: 0.8233 (t0)
REVERT: B  677 TYR cc_start: 0.8846 (m-80) cc_final: 0.8123 (m-80)
REVERT: B  704 CYS cc_start: 0.8265 (p) cc_final: 0.8024 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0661
  time to fit residues: 15.7764
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  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 41 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.095337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.075836 restraints weight = 19810.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.078462 restraints weight = 12897.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.080385 restraints weight = 9443.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.081745 restraints weight = 7445.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.082836 restraints weight = 6227.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.3643

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= 0.132
  Angle     :  0.594   6.582   8928  Z= 0.307
  Chirality :  0.043   0.140   1046
  Planarity :  0.004   0.046   1170
  Dihedral  :  4.353  16.307    918
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.28), residues: 856
  helix:  0.67 (0.28), residues: 348
  sheet: -2.17 (0.43), residues: 136
  loop : -2.84 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 731 
 TYR   0.006   0.001   TYR B 654 
 PHE   0.009   0.001   PHE A 387 
 TRP   0.006   0.001   TRP B 748 
 HIS   0.003   0.001   HIS B 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6594)
  covalent geometry    : angle       0.59391 ( 8928)
  hydrogen bonds       : bond        0.03120 (  290)
  hydrogen bonds       : angle       4.61883 (  840)

*********************** 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
  178 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 LEU cc_start: 0.9358 (pp) cc_final: 0.9049 (mm)
REVERT: A  481 MET cc_start: 0.7930 (mtp) cc_final: 0.7576 (mtp)
REVERT: A  488 LEU cc_start: 0.9327 (tp) cc_final: 0.9060 (tp)
REVERT: A  534 MET cc_start: 0.8765 (tpp) cc_final: 0.8293 (tpp)
REVERT: A  571 HIS cc_start: 0.8455 (m90) cc_final: 0.8138 (m90)
REVERT: A  574 ILE cc_start: 0.9616 (mt) cc_final: 0.9133 (tp)
REVERT: A  575 ASP cc_start: 0.8825 (t0) cc_final: 0.8538 (t0)
REVERT: A  601 MET cc_start: 0.7968 (tmm) cc_final: 0.7093 (tmm)
REVERT: A  677 TYR cc_start: 0.8665 (m-80) cc_final: 0.8098 (m-80)
REVERT: A  704 CYS cc_start: 0.8117 (p) cc_final: 0.7875 (p)
REVERT: B  389 LEU cc_start: 0.9006 (mp) cc_final: 0.8713 (pp)
REVERT: B  481 MET cc_start: 0.8139 (mtp) cc_final: 0.7686 (mtp)
REVERT: B  488 LEU cc_start: 0.9086 (tp) cc_final: 0.8773 (tp)
REVERT: B  516 GLU cc_start: 0.7206 (tt0) cc_final: 0.6838 (tp30)
REVERT: B  534 MET cc_start: 0.8613 (tpp) cc_final: 0.8025 (tpp)
REVERT: B  551 ARG cc_start: 0.9485 (mmm-85) cc_final: 0.9242 (mmm-85)
REVERT: B  558 LEU cc_start: 0.9202 (mt) cc_final: 0.8803 (mt)
REVERT: B  571 HIS cc_start: 0.8544 (m90) cc_final: 0.8218 (m90)
REVERT: B  575 ASP cc_start: 0.8791 (t0) cc_final: 0.8292 (t0)
REVERT: B  660 CYS cc_start: 0.8705 (m) cc_final: 0.8250 (m)
REVERT: B  677 TYR cc_start: 0.8785 (m-80) cc_final: 0.8056 (m-80)
REVERT: B  704 CYS cc_start: 0.8087 (p) cc_final: 0.7847 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.0596
  time to fit residues: 14.6963
Evaluate side-chains
  141 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0370
   chunk 85 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.9862

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

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 = 0.096343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.076647 restraints weight = 19886.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.079362 restraints weight = 12800.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.081281 restraints weight = 9332.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.082744 restraints weight = 7377.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.083835 restraints weight = 6140.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6594  Z= 0.116
  Angle     :  0.599   7.519   8928  Z= 0.310
  Chirality :  0.043   0.145   1046
  Planarity :  0.004   0.046   1170
  Dihedral  :  4.211  14.573    918
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.29), residues: 856
  helix:  0.57 (0.28), residues: 360
  sheet: -2.07 (0.43), residues: 136
  loop : -2.76 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 731 
 TYR   0.008   0.001   TYR A 654 
 PHE   0.006   0.001   PHE A 713 
 TRP   0.007   0.001   TRP A 748 
 HIS   0.008   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6594)
  covalent geometry    : angle       0.59865 ( 8928)
  hydrogen bonds       : bond        0.03055 (  290)
  hydrogen bonds       : angle       4.64836 (  840)

*********************** 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
  175 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.231 
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: 0.7852 (mm-30) cc_final: 0.7509 (mm-30)
REVERT: A  481 MET cc_start: 0.7991 (mtp) cc_final: 0.7634 (mtp)
REVERT: A  488 LEU cc_start: 0.9322 (tp) cc_final: 0.9062 (tp)
REVERT: A  534 MET cc_start: 0.8632 (tpp) cc_final: 0.8213 (tpp)
REVERT: A  571 HIS cc_start: 0.8427 (m90) cc_final: 0.8075 (m90)
REVERT: A  575 ASP cc_start: 0.8814 (t0) cc_final: 0.8581 (t0)
REVERT: A  603 THR cc_start: 0.9139 (t) cc_final: 0.8796 (t)
REVERT: A  660 CYS cc_start: 0.8496 (m) cc_final: 0.8105 (m)
REVERT: A  677 TYR cc_start: 0.8637 (m-80) cc_final: 0.8001 (m-80)
REVERT: A  704 CYS cc_start: 0.8080 (p) cc_final: 0.7833 (p)
REVERT: B  481 MET cc_start: 0.8163 (mtp) cc_final: 0.7601 (mtp)
REVERT: B  488 LEU cc_start: 0.9083 (tp) cc_final: 0.8799 (tp)
REVERT: B  534 MET cc_start: 0.8600 (tpp) cc_final: 0.7990 (tpp)
REVERT: B  537 HIS cc_start: 0.8482 (m90) cc_final: 0.8178 (m90)
REVERT: B  551 ARG cc_start: 0.9456 (mmm-85) cc_final: 0.9226 (mmm-85)
REVERT: B  571 HIS cc_start: 0.8523 (m90) cc_final: 0.8213 (m90)
REVERT: B  575 ASP cc_start: 0.8738 (t0) cc_final: 0.8221 (t0)
REVERT: B  601 MET cc_start: 0.8298 (ptm) cc_final: 0.7648 (ptt)
REVERT: B  660 CYS cc_start: 0.8561 (m) cc_final: 0.8036 (m)
REVERT: B  677 TYR cc_start: 0.8770 (m-80) cc_final: 0.7996 (m-80)
REVERT: B  704 CYS cc_start: 0.7996 (p) cc_final: 0.7785 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0578
  time to fit residues: 13.9746
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  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    0.0970
   chunk 70 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 497 HIS
A 755 HIS
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 HIS
B 559 HIS
B 681 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.096085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.077615 restraints weight = 19505.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.080359 restraints weight = 12338.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.082347 restraints weight = 8832.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.083786 restraints weight = 6868.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.084951 restraints weight = 5647.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6594  Z= 0.133
  Angle     :  0.622   9.955   8928  Z= 0.324
  Chirality :  0.044   0.159   1046
  Planarity :  0.004   0.045   1170
  Dihedral  :  4.219  14.226    918
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.29), residues: 856
  helix:  0.52 (0.28), residues: 360
  sheet: -2.03 (0.44), residues: 136
  loop : -2.66 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 731 
 TYR   0.006   0.001   TYR B 654 
 PHE   0.011   0.001   PHE A 696 
 TRP   0.006   0.001   TRP B 748 
 HIS   0.005   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6594)
  covalent geometry    : angle       0.62195 ( 8928)
  hydrogen bonds       : bond        0.03136 (  290)
  hydrogen bonds       : angle       4.70933 (  840)

*********************** 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
  172 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 LEU cc_start: 0.9313 (pp) cc_final: 0.8993 (mm)
REVERT: A  451 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7604 (mm-30)
REVERT: A  481 MET cc_start: 0.7980 (mtp) cc_final: 0.7556 (mtp)
REVERT: A  507 LYS cc_start: 0.9673 (mtpp) cc_final: 0.9440 (mmmt)
REVERT: A  534 MET cc_start: 0.8604 (tpp) cc_final: 0.8138 (tpp)
REVERT: A  571 HIS cc_start: 0.8415 (m90) cc_final: 0.8062 (m90)
REVERT: A  601 MET cc_start: 0.8097 (ptm) cc_final: 0.7848 (ptm)
REVERT: A  660 CYS cc_start: 0.8547 (m) cc_final: 0.8081 (m)
REVERT: A  677 TYR cc_start: 0.8702 (m-80) cc_final: 0.8128 (m-80)
REVERT: A  704 CYS cc_start: 0.8111 (p) cc_final: 0.7831 (p)
REVERT: B  353 GLU cc_start: 0.8620 (mp0) cc_final: 0.8417 (mp0)
REVERT: B  389 LEU cc_start: 0.8812 (mm) cc_final: 0.8466 (pp)
REVERT: B  481 MET cc_start: 0.8043 (mtp) cc_final: 0.7552 (mtp)
REVERT: B  488 LEU cc_start: 0.9081 (tp) cc_final: 0.8755 (tp)
REVERT: B  534 MET cc_start: 0.8614 (tpp) cc_final: 0.8166 (tpp)
REVERT: B  551 ARG cc_start: 0.9427 (mmm-85) cc_final: 0.9218 (mmm-85)
REVERT: B  558 LEU cc_start: 0.9153 (mt) cc_final: 0.8760 (mt)
REVERT: B  571 HIS cc_start: 0.8553 (m90) cc_final: 0.8225 (m90)
REVERT: B  575 ASP cc_start: 0.8779 (t0) cc_final: 0.8248 (t0)
REVERT: B  601 MET cc_start: 0.8267 (ptm) cc_final: 0.7628 (ptt)
REVERT: B  660 CYS cc_start: 0.8397 (m) cc_final: 0.7848 (m)
REVERT: B  677 TYR cc_start: 0.8740 (m-80) cc_final: 0.8051 (m-80)
REVERT: B  704 CYS cc_start: 0.8022 (p) cc_final: 0.7761 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0684
  time to fit residues: 15.8658
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  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0570
   chunk 63 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 79 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 66 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    1.2104

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.096739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.077590 restraints weight = 19484.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.080324 restraints weight = 12461.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.082333 restraints weight = 9023.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.083841 restraints weight = 7061.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.084950 restraints weight = 5817.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.4379

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= 0.125
  Angle     :  0.621   9.058   8928  Z= 0.321
  Chirality :  0.044   0.154   1046
  Planarity :  0.004   0.045   1170
  Dihedral  :  4.146  14.177    918
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.29), residues: 856
  helix:  0.56 (0.28), residues: 360
  sheet: -2.01 (0.44), residues: 136
  loop : -2.60 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 544 
 TYR   0.008   0.001   TYR A 654 
 PHE   0.008   0.001   PHE A 713 
 TRP   0.007   0.001   TRP B 748 
 HIS   0.004   0.001   HIS B 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6594)
  covalent geometry    : angle       0.62092 ( 8928)
  hydrogen bonds       : bond        0.03086 (  290)
  hydrogen bonds       : angle       4.66180 (  840)

*********************** 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
  168 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 LEU cc_start: 0.9305 (pp) cc_final: 0.9047 (mm)
REVERT: A  451 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7534 (mm-30)
REVERT: A  481 MET cc_start: 0.7893 (mtp) cc_final: 0.7488 (mtp)
REVERT: A  488 LEU cc_start: 0.9161 (tp) cc_final: 0.8887 (tp)
REVERT: A  521 LEU cc_start: 0.9388 (mt) cc_final: 0.9116 (mt)
REVERT: A  534 MET cc_start: 0.8601 (tpp) cc_final: 0.8129 (tpp)
REVERT: A  571 HIS cc_start: 0.8442 (m90) cc_final: 0.8132 (m90)
REVERT: A  601 MET cc_start: 0.8176 (ptm) cc_final: 0.7898 (ptm)
REVERT: A  660 CYS cc_start: 0.8572 (m) cc_final: 0.8038 (m)
REVERT: A  677 TYR cc_start: 0.8645 (m-80) cc_final: 0.8113 (m-80)
REVERT: A  704 CYS cc_start: 0.7997 (p) cc_final: 0.7746 (p)
REVERT: B  353 GLU cc_start: 0.8641 (mp0) cc_final: 0.8364 (mp0)
REVERT: B  389 LEU cc_start: 0.8895 (mm) cc_final: 0.8588 (pp)
REVERT: B  481 MET cc_start: 0.7995 (mtp) cc_final: 0.7581 (mtp)
REVERT: B  488 LEU cc_start: 0.9069 (tp) cc_final: 0.8708 (tp)
REVERT: B  534 MET cc_start: 0.8652 (tpp) cc_final: 0.7947 (tpp)
REVERT: B  551 ARG cc_start: 0.9427 (mmm-85) cc_final: 0.9220 (mmm-85)
REVERT: B  558 LEU cc_start: 0.9147 (mt) cc_final: 0.8855 (mt)
REVERT: B  571 HIS cc_start: 0.8513 (m90) cc_final: 0.8219 (m90)
REVERT: B  575 ASP cc_start: 0.8764 (t0) cc_final: 0.8260 (t0)
REVERT: B  601 MET cc_start: 0.8274 (ptm) cc_final: 0.7601 (ptt)
REVERT: B  660 CYS cc_start: 0.8367 (m) cc_final: 0.7850 (m)
REVERT: B  677 TYR cc_start: 0.8709 (m-80) cc_final: 0.8086 (m-80)
REVERT: B  704 CYS cc_start: 0.7899 (p) cc_final: 0.7669 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0627
  time to fit residues: 14.4268
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  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 69 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 55 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.096548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.077533 restraints weight = 20088.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.080287 restraints weight = 12681.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.082341 restraints weight = 9115.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.083780 restraints weight = 7102.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.085000 restraints weight = 5855.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.4449

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= 0.144
  Angle     :  0.642   9.193   8928  Z= 0.331
  Chirality :  0.044   0.158   1046
  Planarity :  0.004   0.044   1170
  Dihedral  :  4.221  14.838    918
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.29), residues: 856
  helix:  0.50 (0.28), residues: 360
  sheet: -1.99 (0.43), residues: 136
  loop : -2.56 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 544 
 TYR   0.005   0.001   TYR A 654 
 PHE   0.023   0.002   PHE B 616 
 TRP   0.005   0.001   TRP B 748 
 HIS   0.006   0.001   HIS B 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6594)
  covalent geometry    : angle       0.64207 ( 8928)
  hydrogen bonds       : bond        0.03231 (  290)
  hydrogen bonds       : angle       4.75625 (  840)

*********************** 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
  166 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 LEU cc_start: 0.9341 (pp) cc_final: 0.9054 (mm)
REVERT: A  451 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7638 (mm-30)
REVERT: A  481 MET cc_start: 0.7908 (mtp) cc_final: 0.7490 (mtp)
REVERT: A  488 LEU cc_start: 0.9032 (tp) cc_final: 0.8767 (tp)
REVERT: A  534 MET cc_start: 0.8610 (tpp) cc_final: 0.8076 (tpp)
REVERT: A  556 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8456 (tp-100)
REVERT: A  571 HIS cc_start: 0.8427 (m90) cc_final: 0.8092 (m90)
REVERT: A  601 MET cc_start: 0.8191 (ptm) cc_final: 0.7941 (ptm)
REVERT: A  660 CYS cc_start: 0.8556 (m) cc_final: 0.7975 (m)
REVERT: A  677 TYR cc_start: 0.8667 (m-80) cc_final: 0.8122 (m-80)
REVERT: A  704 CYS cc_start: 0.8046 (p) cc_final: 0.7837 (p)
REVERT: B  389 LEU cc_start: 0.8907 (mm) cc_final: 0.8628 (pp)
REVERT: B  481 MET cc_start: 0.8066 (mtp) cc_final: 0.7589 (mtp)
REVERT: B  488 LEU cc_start: 0.9048 (tp) cc_final: 0.8724 (tp)
REVERT: B  534 MET cc_start: 0.8644 (tpp) cc_final: 0.8168 (tpp)
REVERT: B  537 HIS cc_start: 0.8605 (m90) cc_final: 0.8366 (m90)
REVERT: B  558 LEU cc_start: 0.9152 (mt) cc_final: 0.8853 (mt)
REVERT: B  571 HIS cc_start: 0.8527 (m90) cc_final: 0.8205 (m90)
REVERT: B  575 ASP cc_start: 0.8869 (t0) cc_final: 0.8327 (t0)
REVERT: B  601 MET cc_start: 0.8330 (ptm) cc_final: 0.7651 (ptt)
REVERT: B  622 MET cc_start: 0.9163 (tpp) cc_final: 0.8955 (tpt)
REVERT: B  660 CYS cc_start: 0.8402 (m) cc_final: 0.7858 (m)
REVERT: B  677 TYR cc_start: 0.8770 (m-80) cc_final: 0.8090 (m-80)
REVERT: B  704 CYS cc_start: 0.7971 (p) cc_final: 0.7677 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0614
  time to fit residues: 14.2840
Evaluate side-chains
  132 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 72 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   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 = 0.3574 r_free = 0.3574 target = 0.097838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.078542 restraints weight = 19551.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.081350 restraints weight = 12425.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.083411 restraints weight = 8938.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.084864 restraints weight = 6964.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.086066 restraints weight = 5758.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.4738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6594  Z= 0.122
  Angle     :  0.663   9.809   8928  Z= 0.343
  Chirality :  0.044   0.156   1046
  Planarity :  0.004   0.044   1170
  Dihedral  :  4.132  15.832    918
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.29), residues: 856
  helix:  0.49 (0.28), residues: 358
  sheet: -2.00 (0.46), residues: 120
  loop : -2.36 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 551 
 TYR   0.007   0.001   TYR A 654 
 PHE   0.007   0.001   PHE A 642 
 TRP   0.008   0.001   TRP B 748 
 HIS   0.003   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6594)
  covalent geometry    : angle       0.66333 ( 8928)
  hydrogen bonds       : bond        0.03322 (  290)
  hydrogen bonds       : angle       4.83301 (  840)

********************** 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
  173 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 LEU cc_start: 0.9316 (pp) cc_final: 0.9050 (mm)
REVERT: A  451 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7276 (mm-30)
REVERT: A  481 MET cc_start: 0.7872 (mtp) cc_final: 0.7531 (mtp)
REVERT: A  488 LEU cc_start: 0.9031 (tp) cc_final: 0.8809 (tp)
REVERT: A  534 MET cc_start: 0.8610 (tpp) cc_final: 0.8139 (tpp)
REVERT: A  558 LEU cc_start: 0.8984 (mt) cc_final: 0.8699 (mp)
REVERT: A  571 HIS cc_start: 0.8435 (m90) cc_final: 0.8128 (m90)
REVERT: A  601 MET cc_start: 0.8159 (ptm) cc_final: 0.7672 (ptm)
REVERT: A  660 CYS cc_start: 0.8451 (m) cc_final: 0.7791 (m)
REVERT: A  677 TYR cc_start: 0.8621 (m-80) cc_final: 0.8070 (m-80)
REVERT: B  353 GLU cc_start: 0.8638 (mp0) cc_final: 0.8322 (mp0)
REVERT: B  389 LEU cc_start: 0.8875 (mm) cc_final: 0.8553 (pp)
REVERT: B  481 MET cc_start: 0.7744 (mtp) cc_final: 0.7459 (mtp)
REVERT: B  488 LEU cc_start: 0.8884 (tp) cc_final: 0.8611 (tp)
REVERT: B  504 GLU cc_start: 0.9409 (pt0) cc_final: 0.9190 (pp20)
REVERT: B  534 MET cc_start: 0.8675 (tpp) cc_final: 0.7908 (tpp)
REVERT: B  571 HIS cc_start: 0.8477 (m90) cc_final: 0.8193 (m90)
REVERT: B  575 ASP cc_start: 0.8814 (t0) cc_final: 0.8302 (t0)
REVERT: B  601 MET cc_start: 0.8248 (ptm) cc_final: 0.7572 (ptt)
REVERT: B  660 CYS cc_start: 0.8356 (m) cc_final: 0.7785 (m)
REVERT: B  677 TYR cc_start: 0.8703 (m-80) cc_final: 0.8063 (m-80)
REVERT: B  704 CYS cc_start: 0.7681 (p) cc_final: 0.7432 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0617
  time to fit residues: 14.7989
Evaluate side-chains
  132 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 50 optimal weight:    7.9990
   chunk 45 optimal weight:    0.2980
   chunk 35 optimal weight:    4.9990
   chunk 23 optimal weight:    0.1980
   chunk 72 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 67 optimal weight:    0.4980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3578 r_free = 0.3578 target = 0.097375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.078561 restraints weight = 19764.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.081358 restraints weight = 12526.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.083306 restraints weight = 8998.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.084803 restraints weight = 7044.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.085969 restraints weight = 5788.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.4883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6594  Z= 0.117
  Angle     :  0.654   8.334   8928  Z= 0.337
  Chirality :  0.044   0.146   1046
  Planarity :  0.004   0.043   1170
  Dihedral  :  4.067  17.471    918
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.29), residues: 856
  helix:  0.57 (0.29), residues: 358
  sheet: -1.92 (0.47), residues: 120
  loop : -2.22 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 544 
 TYR   0.005   0.001   TYR A 654 
 PHE   0.025   0.002   PHE B 616 
 TRP   0.008   0.001   TRP A 748 
 HIS   0.003   0.001   HIS A 652 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6594)
  covalent geometry    : angle       0.65384 ( 8928)
  hydrogen bonds       : bond        0.03165 (  290)
  hydrogen bonds       : angle       4.70983 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 988.26 seconds
wall clock time: 17 minutes 49.55 seconds (1069.55 seconds total)