Starting phenix.real_space_refine
on Wed Mar  4 04:01:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qma_4593/03_2026/6qma_4593.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qma_4593/03_2026/6qma_4593.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qma_4593/03_2026/6qma_4593.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qma_4593/03_2026/6qma_4593.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qma_4593/03_2026/6qma_4593.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qma_4593/03_2026/6qma_4593.cif"
  }
  resolution = 3.7
  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=   0.001 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     S      40      5.16       5
     C    6970      2.51       5
     N    1786      2.21       5
     O    1916      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10716
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 662, 5356
          Classifications: {'peptide': 662}
          Link IDs: {'PTRANS': 28, 'TRANS': 633}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.55, per 1000 atoms: 0.42
  Number of scatterers: 10716
  At special positions: 0
  Unit cell: (120.428, 110.308, 106.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      4     19.99
     S      40     16.00
     O    1916      8.00
     N    1786      7.00
     C    6970      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: 0.84
  Conformation dependent library (CDL) restraints added in 634.7 milliseconds
  

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2512

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 4 sheets defined
      74.0% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 50
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 3.720A  pdb=" N   HIS A  90 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 111 through 125
    Processing helix  chain 'A' and resid 152 through 166
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 3.827A  pdb=" N   ILE A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 211
      removed outlier: 4.864A  pdb=" N   ILE A 201 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      Proline residue:  A 202  - end of helix
    Processing helix  chain 'A' and resid 217 through 246
      removed outlier: 3.659A  pdb=" N   ALA A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 318
      removed outlier: 4.135A  pdb=" N   ARG A 284 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ILE A 292 " --> pdb=" O   GLN A 288 " (cutoff:3.500A)
      Proline residue:  A 293  - end of helix
    Processing helix  chain 'A' and resid 325 through 358
      Proline residue:  A 332  - end of helix
      Proline residue:  A 341  - end of helix
    Processing helix  chain 'A' and resid 362 through 391
      removed outlier: 6.152A  pdb=" N   ALA A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 415
      removed outlier: 3.673A  pdb=" N   LEU A 404 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 453
      removed outlier: 3.624A  pdb=" N   ASN A 435 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL A 453 " --> pdb=" O   PHE A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 468
    Processing helix  chain 'A' and resid 477 through 481
      removed outlier: 3.507A  pdb=" N   GLU A 480 " --> pdb=" O   GLU A 477 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLU A 481 " --> pdb=" O   ASP A 478 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 477 through 481'
    Processing helix  chain 'A' and resid 482 through 495
      removed outlier: 3.543A  pdb=" N   ARG A 488 " --> pdb=" O   GLU A 484 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR A 494 " --> pdb=" O   ARG A 490 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU A 495 " --> pdb=" O   GLU A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 518
      removed outlier: 3.876A  pdb=" N   SER A 518 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 543
      removed outlier: 4.225A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 585
      removed outlier: 4.152A  pdb=" N   THR A 563 " --> pdb=" O   GLY A 559 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A 574 " --> pdb=" O   TRP A 570 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ASN A 585 " --> pdb=" O   TYR A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 627
    Processing helix  chain 'A' and resid 629 through 650
      removed outlier: 3.937A  pdb=" N   GLN A 633 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 684
      removed outlier: 3.509A  pdb=" N   ILE A 684 " --> pdb=" O   ARG A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 696
    Processing helix  chain 'A' and resid 700 through 718
    Processing helix  chain 'B' and resid 32 through 50
    Processing helix  chain 'B' and resid 72 through 90
      removed outlier: 3.720A  pdb=" N   HIS B  90 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 108
    Processing helix  chain 'B' and resid 111 through 125
    Processing helix  chain 'B' and resid 152 through 166
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.827A  pdb=" N   ILE B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 211
      removed outlier: 4.864A  pdb=" N   ILE B 201 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      Proline residue:  B 202  - end of helix
    Processing helix  chain 'B' and resid 217 through 246
      removed outlier: 3.659A  pdb=" N   ALA B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 318
      removed outlier: 4.134A  pdb=" N   ARG B 284 " --> pdb=" O   PRO B 280 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ILE B 292 " --> pdb=" O   GLN B 288 " (cutoff:3.500A)
      Proline residue:  B 293  - end of helix
    Processing helix  chain 'B' and resid 325 through 358
      Proline residue:  B 332  - end of helix
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 362 through 391
      removed outlier: 6.152A  pdb=" N   ALA B 385 " --> pdb=" O   THR B 381 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 415
      removed outlier: 3.673A  pdb=" N   LEU B 404 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 453
      removed outlier: 3.623A  pdb=" N   ASN B 435 " --> pdb=" O   ALA B 431 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL B 453 " --> pdb=" O   PHE B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 468
    Processing helix  chain 'B' and resid 477 through 481
      removed outlier: 3.508A  pdb=" N   GLU B 480 " --> pdb=" O   GLU B 477 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLU B 481 " --> pdb=" O   ASP B 478 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 477 through 481'
    Processing helix  chain 'B' and resid 482 through 495
      removed outlier: 3.543A  pdb=" N   ARG B 488 " --> pdb=" O   GLU B 484 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR B 494 " --> pdb=" O   ARG B 490 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU B 495 " --> pdb=" O   GLU B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 518
      removed outlier: 3.877A  pdb=" N   SER B 518 " --> pdb=" O   VAL B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 543
      removed outlier: 4.226A  pdb=" N   ALA B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 585
      removed outlier: 4.152A  pdb=" N   THR B 563 " --> pdb=" O   GLY B 559 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE B 574 " --> pdb=" O   TRP B 570 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ASN B 585 " --> pdb=" O   TYR B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 627
    Processing helix  chain 'B' and resid 629 through 650
      removed outlier: 3.937A  pdb=" N   GLN B 633 " --> pdb=" O   SER B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 684
      removed outlier: 3.510A  pdb=" N   ILE B 684 " --> pdb=" O   ARG B 680 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 696
    Processing helix  chain 'B' and resid 700 through 718
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 59
      removed outlier: 4.102A  pdb=" N   SER A  63 " --> pdb=" O   GLY A  59 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266
      removed outlier: 3.708A  pdb=" N   HIS A 265 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 59
      removed outlier: 4.102A  pdb=" N   SER B  63 " --> pdb=" O   GLY B  59 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 266
      removed outlier: 3.707A  pdb=" N   HIS B 265 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)

    746 hydrogen bonds defined for protein.
    2232 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.16 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: 3337
        1.34 -     1.46: 1926
        1.46 -     1.57: 5663
        1.57 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 10992
  Sorted by residual:
  bond pdb=" C   ILE B 292 "
       pdb=" N   PRO B 293 "
    ideal  model  delta    sigma   weight residual
    1.335  1.393 -0.059 1.28e-02 6.10e+03 2.10e+01
  bond pdb=" C   ILE A 292 "
       pdb=" N   PRO A 293 "
    ideal  model  delta    sigma   weight residual
    1.335  1.393 -0.058 1.28e-02 6.10e+03 2.08e+01
  bond pdb=" C   THR A 340 "
       pdb=" N   PRO A 341 "
    ideal  model  delta    sigma   weight residual
    1.335  1.391 -0.055 1.36e-02 5.41e+03 1.67e+01
  bond pdb=" C   THR B 340 "
       pdb=" N   PRO B 341 "
    ideal  model  delta    sigma   weight residual
    1.335  1.391 -0.055 1.36e-02 5.41e+03 1.65e+01
  bond pdb=" C   ILE A 394 "
       pdb=" N   PRO A 395 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.94e+00
  ... (remaining 10987 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 14457
        2.23 -     4.46: 403
        4.46 -     6.69: 30
        6.69 -     8.92: 16
        8.92 -    11.15: 4
  Bond angle restraints: 14910
  Sorted by residual:
  angle pdb=" C   VAL A 454 "
        pdb=" N   VAL A 455 "
        pdb=" CA  VAL A 455 "
      ideal   model   delta    sigma   weight residual
     120.33  124.43   -4.10 8.00e-01 1.56e+00 2.63e+01
  angle pdb=" C   VAL B 454 "
        pdb=" N   VAL B 455 "
        pdb=" CA  VAL B 455 "
      ideal   model   delta    sigma   weight residual
     120.33  124.40   -4.07 8.00e-01 1.56e+00 2.59e+01
  angle pdb=" N   VAL A 248 "
        pdb=" CA  VAL A 248 "
        pdb=" CB  VAL A 248 "
      ideal   model   delta    sigma   weight residual
     112.28  106.95    5.33 1.33e+00 5.65e-01 1.61e+01
  angle pdb=" N   VAL B 248 "
        pdb=" CA  VAL B 248 "
        pdb=" CB  VAL B 248 "
      ideal   model   delta    sigma   weight residual
     112.28  106.95    5.33 1.33e+00 5.65e-01 1.60e+01
  angle pdb=" N   ILE A 543 "
        pdb=" CA  ILE A 543 "
        pdb=" C   ILE A 543 "
      ideal   model   delta    sigma   weight residual
     112.50  107.23    5.27 1.39e+00 5.18e-01 1.44e+01
  ... (remaining 14905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.22: 5694
       17.22 -    34.44: 598
       34.44 -    51.67: 128
       51.67 -    68.89: 20
       68.89 -    86.11: 20
  Dihedral angle restraints: 6460
    sinusoidal: 2592
      harmonic: 3868
  Sorted by residual:
  dihedral pdb=" CA  GLN A 648 "
           pdb=" C   GLN A 648 "
           pdb=" N   GLU A 649 "
           pdb=" CA  GLU A 649 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.35   17.65     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  GLN B 648 "
           pdb=" C   GLN B 648 "
           pdb=" N   GLU B 649 "
           pdb=" CA  GLU B 649 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.35   17.65     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  THR B 135 "
           pdb=" C   THR B 135 "
           pdb=" N   PRO B 136 "
           pdb=" CA  PRO B 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.86  -16.14     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 6457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1253
       0.051 -    0.101: 258
       0.101 -    0.151: 109
       0.151 -    0.202: 8
       0.202 -    0.252: 4
  Chirality restraints: 1632
  Sorted by residual:
  chirality pdb=" CB  VAL A 248 "
            pdb=" CA  VAL A 248 "
            pdb=" CG1 VAL A 248 "
            pdb=" CG2 VAL A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CB  VAL B 248 "
            pdb=" CA  VAL B 248 "
            pdb=" CG1 VAL B 248 "
            pdb=" CG2 VAL B 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CB  VAL B 500 "
            pdb=" CA  VAL B 500 "
            pdb=" CG1 VAL B 500 "
            pdb=" CG2 VAL B 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1629 not shown)

  Planarity restraints: 1894
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 532 "   -0.014 2.00e-02 2.50e+03   2.80e-02 7.82e+00
        pdb=" C   ASN B 532 "    0.048 2.00e-02 2.50e+03
        pdb=" O   ASN B 532 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   TRP B 533 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 532 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.67e+00
        pdb=" C   ASN A 532 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   ASN A 532 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TRP A 533 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 401 "   -0.045 5.00e-02 4.00e+02   6.69e-02 7.16e+00
        pdb=" N   PRO A 402 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 402 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 402 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1891 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 80
        2.56 -     3.14: 8263
        3.14 -     3.73: 17645
        3.73 -     4.31: 22665
        4.31 -     4.90: 37794
  Nonbonded interactions: 86447
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 313 "
            pdb=" OD1 ASN A 317 "
     model   vdw
     1.974 3.040
  nonbonded pdb=" OE2 GLU B 313 "
            pdb=" OD1 ASN B 317 "
     model   vdw
     1.974 3.040
  nonbonded pdb=" OE1 GLN B 445 "
            pdb=" ND2 ASN B 531 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" OE1 GLN A 445 "
            pdb=" ND2 ASN A 531 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   TYR B 120 "
            pdb=" OG1 THR B 124 "
     model   vdw
     2.307 3.040
  ... (remaining 86442 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:             0.950
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.330
  Find NCS groups from input model:        0.070
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
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   0.065  10992  Z= 0.268
  Angle     :  0.880  11.150  14910  Z= 0.508
  Chirality :  0.050   0.252   1632
  Planarity :  0.007   0.067   1894
  Dihedral  : 15.235  86.108   3948
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  7.56 %
    Favored  : 92.27 %
  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: -3.00 (0.18), residues: 1300
  helix: -1.54 (0.13), residues: 934
  sheet: -2.21 (0.62), residues: 68
  loop : -2.77 (0.29), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 549 
 TYR   0.021   0.002   TYR B 279 
 PHE   0.032   0.002   PHE A 396 
 TRP   0.027   0.002   TRP B 235 
 HIS   0.006   0.001   HIS B 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 (10992)
  covalent geometry    : angle       0.88009 (14910)
  hydrogen bonds       : bond        0.11760 (  746)
  hydrogen bonds       : angle       6.07795 ( 2232)

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

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

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 167
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7960 (tpp80)
  outliers start: 2
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1226
  time to fit residues: 27.7976
Evaluate side-chains
  119 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 317 ASN
A 378 ASN
A 435 ASN
A 641 GLN
A 648 GLN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 HIS
B 317 ASN
B 378 ASN
B 435 ASN
B 641 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.109671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.082997 restraints weight = 24293.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.085522 restraints weight = 12730.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.087126 restraints weight = 8798.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.088017 restraints weight = 7193.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.088422 restraints weight = 6464.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10992  Z= 0.145
  Angle     :  0.569   8.287  14910  Z= 0.301
  Chirality :  0.038   0.130   1632
  Planarity :  0.005   0.050   1894
  Dihedral  :  4.431  15.868   1422
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 13.09 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.55 (0.22), residues: 1300
  helix:  0.41 (0.15), residues: 936
  sheet: -1.89 (0.67), residues: 68
  loop : -2.24 (0.32), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  45 
 TYR   0.017   0.002   TYR B  26 
 PHE   0.013   0.001   PHE B 396 
 TRP   0.016   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10992)
  covalent geometry    : angle       0.56878 (14910)
  hydrogen bonds       : bond        0.04966 (  746)
  hydrogen bonds       : angle       4.52848 ( 2232)

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

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

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8549 (t0)
REVERT: A  384 MET cc_start: 0.8540 (tpp) cc_final: 0.8133 (mpp)
REVERT: A  482 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7709 (mt-10)
REVERT: A  523 LEU cc_start: 0.8915 (mp) cc_final: 0.8558 (mp)
REVERT: B  378 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8567 (t0)
REVERT: B  482 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7701 (mt-10)
REVERT: B  638 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7807 (tm-30)
  outliers start: 24
  outliers final: 12
  residues processed: 156
  average time/residue: 0.1067
  time to fit residues: 23.5935
Evaluate side-chains
  140 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  378 ASN
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  644 LYS
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0770
   chunk 0 optimal weight:    8.9990
   chunk 83 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 92 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 120 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    2.3744

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 156 ASN
A 378 ASN
A 641 GLN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 ASN
B 378 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.107471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.080472 restraints weight = 24730.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.082900 restraints weight = 13180.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.084368 restraints weight = 9225.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.085266 restraints weight = 7617.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.085639 restraints weight = 6851.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10992  Z= 0.199
  Angle     :  0.574   7.086  14910  Z= 0.306
  Chirality :  0.039   0.128   1632
  Planarity :  0.004   0.043   1894
  Dihedral  :  4.207  15.073   1422
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.03 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.44 (0.23), residues: 1300
  helix:  1.13 (0.16), residues: 940
  sheet: -1.72 (0.67), residues: 68
  loop : -1.88 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 432 
 TYR   0.016   0.002   TYR B  26 
 PHE   0.018   0.001   PHE B 335 
 TRP   0.016   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (10992)
  covalent geometry    : angle       0.57400 (14910)
  hydrogen bonds       : bond        0.04900 (  746)
  hydrogen bonds       : angle       4.41389 ( 2232)

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

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

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 116
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.8818 (t) cc_final: 0.8378 (p)
REVERT: A  482 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7860 (mt-10)
REVERT: B  203 SER cc_start: 0.8815 (t) cc_final: 0.8421 (p)
REVERT: B  638 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7567 (tm-30)
  outliers start: 34
  outliers final: 22
  residues processed: 138
  average time/residue: 0.0836
  time to fit residues: 17.6270
Evaluate side-chains
  136 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  378 ASN
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 26 optimal weight:    9.9990
   chunk 60 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 102 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
A 510 GLN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.106815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.079808 restraints weight = 25061.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.082231 restraints weight = 13314.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.083680 restraints weight = 9333.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.084546 restraints weight = 7711.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.084767 restraints weight = 6953.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10992  Z= 0.197
  Angle     :  0.573   6.752  14910  Z= 0.303
  Chirality :  0.039   0.128   1632
  Planarity :  0.004   0.044   1894
  Dihedral  :  4.119  14.271   1422
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.64 %
    Favored  : 80.93 %
  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:  0.89 (0.23), residues: 1300
  helix:  1.50 (0.16), residues: 938
  sheet: -1.68 (0.67), residues: 68
  loop : -1.78 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 645 
 TYR   0.017   0.002   TYR B  26 
 PHE   0.014   0.001   PHE B 189 
 TRP   0.018   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (10992)
  covalent geometry    : angle       0.57321 (14910)
  hydrogen bonds       : bond        0.04819 (  746)
  hydrogen bonds       : angle       4.34969 ( 2232)

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

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

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 117
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7961 (t0)
REVERT: A  203 SER cc_start: 0.8830 (t) cc_final: 0.8344 (p)
REVERT: A  384 MET cc_start: 0.8668 (tpp) cc_final: 0.7860 (mpp)
REVERT: B  173 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8024 (t0)
REVERT: B  203 SER cc_start: 0.8846 (t) cc_final: 0.8407 (p)
REVERT: B  378 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8544 (t0)
REVERT: B  638 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7304 (mp0)
  outliers start: 39
  outliers final: 26
  residues processed: 141
  average time/residue: 0.0803
  time to fit residues: 17.8861
Evaluate side-chains
  139 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  639 ARG
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 76 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0270
   chunk 31 optimal weight:    6.9990
   chunk 93 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 111 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    1.3042

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN
B 510 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.107936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.080989 restraints weight = 24593.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.083442 restraints weight = 13198.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.084927 restraints weight = 9261.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.085824 restraints weight = 7629.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.086109 restraints weight = 6867.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10992  Z= 0.140
  Angle     :  0.534   5.938  14910  Z= 0.280
  Chirality :  0.038   0.130   1632
  Planarity :  0.004   0.044   1894
  Dihedral  :  4.022  14.344   1422
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.87 %
    Favored  : 80.14 %
  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:  1.24 (0.23), residues: 1300
  helix:  1.73 (0.16), residues: 940
  sheet: -1.47 (0.70), residues: 68
  loop : -1.61 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  45 
 TYR   0.015   0.002   TYR B  26 
 PHE   0.019   0.001   PHE B 335 
 TRP   0.018   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10992)
  covalent geometry    : angle       0.53419 (14910)
  hydrogen bonds       : bond        0.04551 (  746)
  hydrogen bonds       : angle       4.22820 ( 2232)

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

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

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7923 (t0)
REVERT: A  203 SER cc_start: 0.8844 (t) cc_final: 0.8459 (p)
REVERT: A  378 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8541 (t0)
REVERT: A  384 MET cc_start: 0.8674 (tpp) cc_final: 0.7940 (mpp)
REVERT: A  575 THR cc_start: 0.9194 (m) cc_final: 0.8949 (p)
REVERT: B  173 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7940 (t0)
REVERT: B  203 SER cc_start: 0.8809 (t) cc_final: 0.8415 (p)
REVERT: B  565 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9038 (mp)
REVERT: B  638 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7500 (tm-30)
  outliers start: 34
  outliers final: 23
  residues processed: 151
  average time/residue: 0.0818
  time to fit residues: 19.0723
Evaluate side-chains
  142 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  378 ASN
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  639 ARG
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 85 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9980
   chunk 96 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 101 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 90 optimal weight:    8.9990
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.107950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.081066 restraints weight = 24843.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.083531 restraints weight = 13256.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.085017 restraints weight = 9287.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.085896 restraints weight = 7649.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.086121 restraints weight = 6903.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10992  Z= 0.145
  Angle     :  0.536   6.200  14910  Z= 0.280
  Chirality :  0.038   0.130   1632
  Planarity :  0.004   0.045   1894
  Dihedral  :  3.927  13.434   1422
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 17.75 %
    Favored  : 78.91 %
  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:  1.46 (0.24), residues: 1300
  helix:  1.90 (0.16), residues: 938
  sheet: -1.32 (0.72), residues: 68
  loop : -1.55 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 548 
 TYR   0.015   0.002   TYR B  26 
 PHE   0.010   0.001   PHE A 196 
 TRP   0.018   0.001   TRP A 235 
 HIS   0.002   0.001   HIS B 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10992)
  covalent geometry    : angle       0.53601 (14910)
  hydrogen bonds       : bond        0.04448 (  746)
  hydrogen bonds       : angle       4.17257 ( 2232)

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

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

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 120
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7925 (t0)
REVERT: A  203 SER cc_start: 0.8830 (t) cc_final: 0.8405 (p)
REVERT: A  384 MET cc_start: 0.8680 (tpp) cc_final: 0.7997 (mpp)
REVERT: A  565 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9052 (mp)
REVERT: B  173 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7942 (t0)
REVERT: B  203 SER cc_start: 0.8813 (t) cc_final: 0.8419 (p)
REVERT: B  384 MET cc_start: 0.8684 (tpp) cc_final: 0.7956 (mpp)
REVERT: B  565 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9062 (mp)
REVERT: B  638 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7513 (tm-30)
  outliers start: 38
  outliers final: 29
  residues processed: 145
  average time/residue: 0.0804
  time to fit residues: 18.1622
Evaluate side-chains
  150 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 117
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  639 ARG
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 103 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0870
   chunk 72 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    3.4164

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
A 531 ASN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.104632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.077906 restraints weight = 24931.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.080199 restraints weight = 13550.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.081647 restraints weight = 9583.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.082497 restraints weight = 7943.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.082654 restraints weight = 7162.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  10992  Z= 0.262
  Angle     :  0.628   6.587  14910  Z= 0.331
  Chirality :  0.041   0.134   1632
  Planarity :  0.004   0.046   1894
  Dihedral  :  4.079  15.102   1422
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 18.45 %
    Favored  : 77.50 %
  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:  1.32 (0.24), residues: 1300
  helix:  1.79 (0.16), residues: 942
  sheet: -1.29 (0.74), residues: 66
  loop : -1.68 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 548 
 TYR   0.019   0.002   TYR B  26 
 PHE   0.021   0.002   PHE A 189 
 TRP   0.016   0.002   TRP A 235 
 HIS   0.005   0.001   HIS B 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 (10992)
  covalent geometry    : angle       0.62794 (14910)
  hydrogen bonds       : bond        0.05018 (  746)
  hydrogen bonds       : angle       4.37744 ( 2232)

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

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

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 111
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8034 (t0)
REVERT: A  203 SER cc_start: 0.8887 (t) cc_final: 0.8447 (p)
REVERT: A  378 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8509 (t0)
REVERT: A  384 MET cc_start: 0.8765 (tpp) cc_final: 0.8085 (mpp)
REVERT: A  565 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9069 (mp)
REVERT: B  173 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8040 (t0)
REVERT: B  203 SER cc_start: 0.8811 (t) cc_final: 0.8369 (p)
REVERT: B  378 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8275 (m-40)
REVERT: B  384 MET cc_start: 0.8741 (tpp) cc_final: 0.8031 (mpp)
REVERT: B  638 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7303 (mp0)
  outliers start: 46
  outliers final: 34
  residues processed: 144
  average time/residue: 0.0819
  time to fit residues: 17.8429
Evaluate side-chains
  146 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 107
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  378 ASN
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  639 ARG
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  666 HIS
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 127 optimal weight:    9.9990
   chunk 23 optimal weight:    0.5980
   chunk 89 optimal weight:    0.7980
   chunk 130 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9980
   chunk 112 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 131 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 ASN
B 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.107578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.080808 restraints weight = 24652.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.083248 restraints weight = 13354.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.084711 restraints weight = 9409.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.085592 restraints weight = 7766.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.085958 restraints weight = 7002.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10992  Z= 0.136
  Angle     :  0.547   8.357  14910  Z= 0.285
  Chirality :  0.038   0.135   1632
  Planarity :  0.004   0.045   1894
  Dihedral  :  3.983  13.554   1422
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.95 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.59 (0.24), residues: 1300
  helix:  1.99 (0.16), residues: 940
  sheet: -1.03 (0.74), residues: 68
  loop : -1.58 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 505 
 TYR   0.015   0.002   TYR B  26 
 PHE   0.022   0.001   PHE B 335 
 TRP   0.021   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10992)
  covalent geometry    : angle       0.54727 (14910)
  hydrogen bonds       : bond        0.04534 (  746)
  hydrogen bonds       : angle       4.17376 ( 2232)

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

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

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 120
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7890 (t0)
REVERT: A  378 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8449 (t0)
REVERT: A  384 MET cc_start: 0.8684 (tpp) cc_final: 0.8008 (mpp)
REVERT: A  565 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9067 (mp)
REVERT: A  575 THR cc_start: 0.9199 (m) cc_final: 0.8971 (p)
REVERT: A  638 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8258 (tm-30)
REVERT: B  203 SER cc_start: 0.8846 (t) cc_final: 0.8451 (p)
REVERT: B  378 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8408 (t0)
REVERT: B  384 MET cc_start: 0.8669 (tpp) cc_final: 0.8026 (mpp)
REVERT: B  565 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9072 (mp)
REVERT: B  575 THR cc_start: 0.9203 (m) cc_final: 0.8970 (p)
REVERT: B  638 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7277 (mp0)
  outliers start: 37
  outliers final: 27
  residues processed: 147
  average time/residue: 0.0840
  time to fit residues: 19.1658
Evaluate side-chains
  146 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  378 ASN
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  639 ARG
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  156 ASN
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 112 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0010
   chunk 80 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 ASN
B 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.107705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.081066 restraints weight = 24526.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.083478 restraints weight = 13317.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.084950 restraints weight = 9385.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.085841 restraints weight = 7742.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.086132 restraints weight = 6979.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10992  Z= 0.139
  Angle     :  0.544   8.461  14910  Z= 0.282
  Chirality :  0.038   0.138   1632
  Planarity :  0.004   0.045   1894
  Dihedral  :  3.911  13.025   1422
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.74 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.71 (0.24), residues: 1300
  helix:  2.08 (0.16), residues: 938
  sheet: -0.93 (0.74), residues: 68
  loop : -1.52 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  45 
 TYR   0.026   0.002   TYR A  81 
 PHE   0.020   0.001   PHE B 335 
 TRP   0.021   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10992)
  covalent geometry    : angle       0.54356 (14910)
  hydrogen bonds       : bond        0.04443 (  746)
  hydrogen bonds       : angle       4.13268 ( 2232)

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

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

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 121
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7931 (t0)
REVERT: A  378 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8510 (t0)
REVERT: A  384 MET cc_start: 0.8676 (tpp) cc_final: 0.7996 (mpp)
REVERT: A  565 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9064 (mp)
REVERT: A  575 THR cc_start: 0.9190 (m) cc_final: 0.8956 (p)
REVERT: A  638 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8255 (tm-30)
REVERT: B  203 SER cc_start: 0.8785 (t) cc_final: 0.8388 (p)
REVERT: B  378 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8485 (t0)
REVERT: B  384 MET cc_start: 0.8669 (tpp) cc_final: 0.7981 (mpp)
REVERT: B  565 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9052 (mp)
REVERT: B  575 THR cc_start: 0.9189 (m) cc_final: 0.8954 (p)
REVERT: B  638 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7501 (tm-30)
  outliers start: 36
  outliers final: 29
  residues processed: 147
  average time/residue: 0.0806
  time to fit residues: 18.4236
Evaluate side-chains
  147 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  378 ASN
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  639 ARG
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  156 ASN
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 25 optimal weight:    0.0000
   chunk 111 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0070
   chunk 121 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.8008

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 ASN
B 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.108200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.081779 restraints weight = 24580.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.084206 restraints weight = 13237.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.085707 restraints weight = 9309.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.086288 restraints weight = 7660.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.086965 restraints weight = 7010.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10992  Z= 0.127
  Angle     :  0.549   8.612  14910  Z= 0.281
  Chirality :  0.038   0.142   1632
  Planarity :  0.004   0.044   1894
  Dihedral  :  3.872  12.790   1422
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.74 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.81 (0.24), residues: 1300
  helix:  2.15 (0.16), residues: 938
  sheet: -0.87 (0.74), residues: 68
  loop : -1.48 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  45 
 TYR   0.014   0.001   TYR B  26 
 PHE   0.022   0.001   PHE B 335 
 TRP   0.021   0.001   TRP B 235 
 HIS   0.002   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10992)
  covalent geometry    : angle       0.54859 (14910)
  hydrogen bonds       : bond        0.04321 (  746)
  hydrogen bonds       : angle       4.08099 ( 2232)

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

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

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2600 Ramachandran restraints generated.
    1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 117
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8504 (t0)
REVERT: A  384 MET cc_start: 0.8660 (tpp) cc_final: 0.7962 (mpp)
REVERT: A  565 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9043 (mp)
REVERT: A  575 THR cc_start: 0.9171 (m) cc_final: 0.8936 (p)
REVERT: A  638 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8233 (tm-30)
REVERT: B  203 SER cc_start: 0.8709 (t) cc_final: 0.8349 (p)
REVERT: B  378 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8517 (t0)
REVERT: B  384 MET cc_start: 0.8656 (tpp) cc_final: 0.7982 (mpp)
REVERT: B  565 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9044 (mp)
REVERT: B  575 THR cc_start: 0.9171 (m) cc_final: 0.8929 (p)
REVERT: B  638 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7528 (tm-30)
  outliers start: 36
  outliers final: 31
  residues processed: 142
  average time/residue: 0.0739
  time to fit residues: 16.2988
Evaluate side-chains
  150 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 115
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  378 ASN
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  639 ARG
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  156 ASN
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain B residue  639 ARG
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 108 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 124 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 84 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 ASN
B 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.108042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.081531 restraints weight = 24929.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.083948 restraints weight = 13405.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.085480 restraints weight = 9410.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.086356 restraints weight = 7725.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.086716 restraints weight = 6945.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10992  Z= 0.134
  Angle     :  0.552   8.374  14910  Z= 0.282
  Chirality :  0.038   0.139   1632
  Planarity :  0.004   0.044   1894
  Dihedral  :  3.828  12.643   1422
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.91 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.24), residues: 1300
  helix:  2.19 (0.16), residues: 938
  sheet: -0.84 (0.74), residues: 68
  loop : -1.44 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  45 
 TYR   0.014   0.002   TYR B  26 
 PHE   0.021   0.001   PHE B 335 
 TRP   0.020   0.001   TRP B 235 
 HIS   0.002   0.001   HIS B 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10992)
  covalent geometry    : angle       0.55199 (14910)
  hydrogen bonds       : bond        0.04286 (  746)
  hydrogen bonds       : angle       4.06092 ( 2232)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1678.44 seconds
wall clock time: 29 minutes 43.67 seconds (1783.67 seconds total)