Starting phenix.real_space_refine
on Fri Feb 14 22:00:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qma_4593/02_2025/6qma_4593.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qma_4593/02_2025/6qma_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_4593/02_2025/6qma_4593.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qma_4593/02_2025/6qma_4593.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qma_4593/02_2025/6qma_4593.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qma_4593/02_2025/6qma_4593.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 10.28, per 1000 atoms: 0.96
  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: 2.58
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 1.04
  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: 3.03

  Time building geometry restraints manager: 3.01 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: 0.05
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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     29.390
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.430
-------------------------------------------------------------------------------
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= 0.356
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (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
 TRP   0.027   0.002   TRP B 235 
 HIS   0.006   0.001   HIS B 143 
 PHE   0.032   0.002   PHE A 396 
 TYR   0.021   0.002   TYR B 279 
 ARG   0.004   0.001   ARG A 549 

*********************** 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  : 1.169 
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: 0.2748
  time to fit residues: 62.1750
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  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.9990
   chunk 100 optimal weight:    8.9990
   chunk 55 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 67 optimal weight:   10.0000
   chunk 53 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 62 optimal weight:   20.0000
   chunk 77 optimal weight:    7.9990
   chunk 119 optimal weight:    0.8980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 151 HIS
A 156 ASN
A 317 ASN
A 378 ASN
A 435 ASN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 HIS
B 156 ASN
B 317 ASN
B 378 ASN
B 435 ASN
B 641 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.109108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.082384 restraints weight = 24234.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.084899 restraints weight = 12757.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.086459 restraints weight = 8851.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10992  Z= 0.203
  Angle     :  0.571   7.892  14910  Z= 0.303
  Chirality :  0.038   0.135   1632
  Planarity :  0.005   0.049   1894
  Dihedral  :  4.395  15.809   1422
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.09 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.22), residues: 1300
  helix:  0.45 (0.15), residues: 936
  sheet: -1.87 (0.67), residues: 68
  loop : -2.22 (0.32), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.014   0.001   PHE B 396 
 TYR   0.017   0.002   TYR B  26 
 ARG   0.004   0.000   ARG B  45 

*********************** 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
  165 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 1.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8557 (t0)
REVERT: A  384 MET cc_start: 0.8558 (tpp) cc_final: 0.8203 (mpp)
REVERT: A  482 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7723 (mt-10)
REVERT: B  482 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7881 (mt-10)
  outliers start: 28
  outliers final: 16
  residues processed: 158
  average time/residue: 0.2282
  time to fit residues: 51.8757
Evaluate side-chains
  138 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  244 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  300 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  482 GLU
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  244 VAL
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  482 GLU
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 96 optimal weight:    0.0000
   chunk 46 optimal weight:    7.9990
   chunk 117 optimal weight:    4.9990
   chunk 81 optimal weight:    8.9990
   chunk 63 optimal weight:    0.0770
   chunk 84 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 110 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 123 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    2.4148

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.107007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.079891 restraints weight = 24853.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.082308 restraints weight = 13293.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.083829 restraints weight = 9349.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1922

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= 0.284
  Angle     :  0.579   6.946  14910  Z= 0.309
  Chirality :  0.039   0.130   1632
  Planarity :  0.004   0.044   1894
  Dihedral  :  4.197  15.284   1422
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 14.85 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.23), residues: 1300
  helix:  1.19 (0.16), residues: 938
  sheet: -1.71 (0.67), residues: 68
  loop : -1.92 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 479 
 PHE   0.018   0.001   PHE B 335 
 TYR   0.017   0.002   TYR B  26 
 ARG   0.003   0.000   ARG B  45 

*********************** 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
  157 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 117
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7949 (t0)
REVERT: A  203 SER cc_start: 0.8845 (t) cc_final: 0.8429 (p)
REVERT: B  173 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8012 (t0)
REVERT: B  203 SER cc_start: 0.8797 (t) cc_final: 0.8383 (p)
REVERT: B  378 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8343 (m-40)
  outliers start: 40
  outliers final: 25
  residues processed: 145
  average time/residue: 0.1928
  time to fit residues: 42.8256
Evaluate side-chains
  141 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
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  527 CYS
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   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  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  378 ASN
Chi-restraints excluded: chain B residue  527 CYS
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 72 optimal weight:    7.9990
   chunk 105 optimal weight:    9.9990
   chunk 129 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 108 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 120 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  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
B 510 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.105930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.078995 restraints weight = 24703.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.081337 restraints weight = 13299.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.082816 restraints weight = 9390.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10992  Z= 0.319
  Angle     :  0.589   6.119  14910  Z= 0.312
  Chirality :  0.040   0.130   1632
  Planarity :  0.004   0.045   1894
  Dihedral  :  4.147  14.789   1422
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 15.73 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.23), residues: 1300
  helix:  1.45 (0.16), residues: 942
  sheet: -1.66 (0.67), residues: 68
  loop : -1.81 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B 479 
 PHE   0.015   0.001   PHE B 189 
 TYR   0.018   0.002   TYR B  26 
 ARG   0.002   0.000   ARG B  45 

*********************** 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
  158 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 115
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7974 (t0)
REVERT: A  203 SER cc_start: 0.8887 (t) cc_final: 0.8460 (p)
REVERT: A  378 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8544 (t0)
REVERT: A  384 MET cc_start: 0.8721 (tpp) cc_final: 0.7965 (mpp)
REVERT: B  173 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8007 (t0)
REVERT: B  203 SER cc_start: 0.8848 (t) cc_final: 0.8415 (p)
  outliers start: 43
  outliers final: 35
  residues processed: 143
  average time/residue: 0.1853
  time to fit residues: 41.0614
Evaluate side-chains
  148 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 110
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
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  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  440 PHE
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  527 CYS
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   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  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  527 CYS
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 100 optimal weight:   10.0000
   chunk 129 optimal weight:    0.1980
   chunk 103 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 128 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 131 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   overall best weight:    1.8186

-------------------------------------------------------------------------------
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
B 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.106941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.080082 restraints weight = 24586.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.082448 restraints weight = 13173.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.083923 restraints weight = 9294.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10992  Z= 0.236
  Angle     :  0.553   5.838  14910  Z= 0.291
  Chirality :  0.039   0.130   1632
  Planarity :  0.004   0.044   1894
  Dihedral  :  4.078  14.777   1422
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 17.05 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.23), residues: 1300
  helix:  1.66 (0.16), residues: 940
  sheet: -1.52 (0.69), residues: 68
  loop : -1.72 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B  58 
 PHE   0.018   0.001   PHE B 335 
 TYR   0.017   0.002   TYR B  26 
 ARG   0.002   0.000   ARG B 548 

*********************** 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
  157 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 117
  time to evaluate  : 1.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7966 (t0)
REVERT: A  203 SER cc_start: 0.8867 (t) cc_final: 0.8427 (p)
REVERT: A  384 MET cc_start: 0.8720 (tpp) cc_final: 0.8012 (mpp)
REVERT: A  638 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8350 (tm-30)
REVERT: B  173 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7962 (t0)
REVERT: B  203 SER cc_start: 0.8842 (t) cc_final: 0.8450 (p)
REVERT: B  378 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8549 (t0)
  outliers start: 40
  outliers final: 29
  residues processed: 144
  average time/residue: 0.1997
  time to fit residues: 44.1776
Evaluate side-chains
  143 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
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  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  527 CYS
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   66 VAL
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  200 VAL
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  527 CYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   chunk 90 optimal weight:    8.9990
   chunk 111 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    8.9990
   chunk 68 optimal weight:    8.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 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 = 0.107592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.080801 restraints weight = 24745.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.083234 restraints weight = 13210.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.084720 restraints weight = 9246.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10992  Z= 0.202
  Angle     :  0.538   6.496  14910  Z= 0.282
  Chirality :  0.038   0.132   1632
  Planarity :  0.004   0.044   1894
  Dihedral  :  3.974  13.095   1422
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 17.66 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.23), residues: 1300
  helix:  1.79 (0.16), residues: 940
  sheet: -1.31 (0.71), residues: 68
  loop : -1.62 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 265 
 PHE   0.012   0.001   PHE A 640 
 TYR   0.015   0.002   TYR B  26 
 ARG   0.002   0.000   ARG B 548 

*********************** 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
  165 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 122
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.8878 (t) cc_final: 0.8526 (p)
REVERT: A  378 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8484 (t0)
REVERT: A  384 MET cc_start: 0.8732 (tpp) cc_final: 0.8040 (mpp)
REVERT: A  565 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9052 (mp)
REVERT: A  638 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8344 (tm-30)
REVERT: B  203 SER cc_start: 0.8873 (t) cc_final: 0.8539 (p)
REVERT: B  384 MET cc_start: 0.8699 (tpp) cc_final: 0.7991 (mpp)
REVERT: B  565 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9093 (mp)
  outliers start: 43
  outliers final: 33
  residues processed: 152
  average time/residue: 0.1929
  time to fit residues: 45.3987
Evaluate side-chains
  149 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 1.475 
-------------------------------------------------------------------------------
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  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   49 THR
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  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  527 CYS
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  639 ARG
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 126 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   chunk 115 optimal weight:    6.9990
   chunk 117 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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
B 156 ASN
B 378 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.108329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.081545 restraints weight = 24839.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.084014 restraints weight = 13309.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.085501 restraints weight = 9316.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2447

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= 0.172
  Angle     :  0.527   5.811  14910  Z= 0.274
  Chirality :  0.037   0.132   1632
  Planarity :  0.004   0.045   1894
  Dihedral  :  3.890  12.409   1422
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.33 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.24), residues: 1300
  helix:  1.92 (0.16), residues: 940
  sheet: -1.18 (0.74), residues: 68
  loop : -1.54 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 265 
 PHE   0.020   0.001   PHE B 335 
 TYR   0.014   0.001   TYR B  26 
 ARG   0.001   0.000   ARG B  45 

*********************** 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
  165 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 128
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.8867 (t) cc_final: 0.8531 (p)
REVERT: A  384 MET cc_start: 0.8690 (tpp) cc_final: 0.7963 (mpp)
REVERT: A  439 TYR cc_start: 0.7454 (m-80) cc_final: 0.6874 (m-80)
REVERT: A  565 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9059 (mp)
REVERT: A  575 THR cc_start: 0.9184 (m) cc_final: 0.8941 (p)
REVERT: B  203 SER cc_start: 0.8800 (t) cc_final: 0.8475 (p)
REVERT: B  378 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8484 (t0)
REVERT: B  384 MET cc_start: 0.8704 (tpp) cc_final: 0.7951 (mpp)
REVERT: B  565 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9094 (mp)
REVERT: B  575 THR cc_start: 0.9184 (m) cc_final: 0.8939 (p)
  outliers start: 37
  outliers final: 25
  residues processed: 156
  average time/residue: 0.2086
  time to fit residues: 49.1038
Evaluate side-chains
  144 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  156 ASN
Chi-restraints excluded: chain A residue  240 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  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  211 LEU
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  240 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  451 THR
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  639 ARG
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 38 optimal weight:    0.0870
   chunk 125 optimal weight:    5.9990
   chunk 117 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 123 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 101 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 113 optimal weight:    0.2980
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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
B 156 ASN
B 378 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.109278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.082589 restraints weight = 24606.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.085058 restraints weight = 13222.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.086564 restraints weight = 9283.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10992  Z= 0.158
  Angle     :  0.535   7.818  14910  Z= 0.275
  Chirality :  0.037   0.136   1632
  Planarity :  0.004   0.044   1894
  Dihedral  :  3.828  12.185   1422
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.39 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.24), residues: 1300
  helix:  2.06 (0.16), residues: 940
  sheet: -1.09 (0.75), residues: 68
  loop : -1.47 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 265 
 PHE   0.022   0.001   PHE B 335 
 TYR   0.014   0.001   TYR A 439 
 ARG   0.002   0.000   ARG B  45 

*********************** 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
  161 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 127
  time to evaluate  : 1.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8479 (t0)
REVERT: A  384 MET cc_start: 0.8679 (tpp) cc_final: 0.7952 (mpp)
REVERT: A  565 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9048 (mp)
REVERT: A  575 THR cc_start: 0.9147 (m) cc_final: 0.8909 (p)
REVERT: B  378 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8514 (t0)
REVERT: B  384 MET cc_start: 0.8646 (tpp) cc_final: 0.7938 (mpp)
REVERT: B  437 MET cc_start: 0.9390 (tpp) cc_final: 0.9056 (tpp)
REVERT: B  565 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9068 (mp)
REVERT: B  575 THR cc_start: 0.9148 (m) cc_final: 0.8909 (p)
  outliers start: 34
  outliers final: 26
  residues processed: 153
  average time/residue: 0.1842
  time to fit residues: 43.4230
Evaluate side-chains
  151 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  156 ASN
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  252 SER
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  336 LEU
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  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  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  336 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 12 optimal weight:    0.0470
   chunk 79 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.6878

-------------------------------------------------------------------------------
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
B 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.109353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.082787 restraints weight = 24928.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.085247 restraints weight = 13335.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.086819 restraints weight = 9318.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10992  Z= 0.165
  Angle     :  0.539   7.346  14910  Z= 0.276
  Chirality :  0.037   0.143   1632
  Planarity :  0.004   0.044   1894
  Dihedral  :  3.780  12.015   1422
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.91 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.24), residues: 1300
  helix:  2.12 (0.16), residues: 940
  sheet: -1.04 (0.74), residues: 68
  loop : -1.42 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 265 
 PHE   0.021   0.001   PHE B 335 
 TYR   0.012   0.001   TYR B  26 
 ARG   0.002   0.000   ARG B  45 

*********************** 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
  158 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  384 MET cc_start: 0.8690 (tpp) cc_final: 0.7970 (mpp)
REVERT: A  565 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9038 (mp)
REVERT: A  575 THR cc_start: 0.9144 (m) cc_final: 0.8897 (p)
REVERT: B  384 MET cc_start: 0.8675 (tpp) cc_final: 0.7924 (mpp)
REVERT: B  437 MET cc_start: 0.9364 (tpp) cc_final: 0.9054 (tpp)
REVERT: B  565 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9055 (mp)
REVERT: B  575 THR cc_start: 0.9159 (m) cc_final: 0.8904 (p)
  outliers start: 33
  outliers final: 26
  residues processed: 152
  average time/residue: 0.1911
  time to fit residues: 44.2416
Evaluate side-chains
  150 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  252 SER
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  336 LEU
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  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  336 LEU
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  666 HIS
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 78 optimal weight:    0.3980
   chunk 100 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 75 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 115 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    1.8786

-------------------------------------------------------------------------------
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 378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.107540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.081066 restraints weight = 24771.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.083450 restraints weight = 13402.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.084920 restraints weight = 9447.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10992  Z= 0.242
  Angle     :  0.577   8.106  14910  Z= 0.296
  Chirality :  0.038   0.160   1632
  Planarity :  0.004   0.044   1894
  Dihedral  :  3.782  11.695   1422
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.00 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.24), residues: 1300
  helix:  2.17 (0.16), residues: 942
  sheet: -1.02 (0.76), residues: 66
  loop : -1.45 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 235 
 HIS   0.003   0.001   HIS B 479 
 PHE   0.020   0.001   PHE B 335 
 TYR   0.015   0.002   TYR A 383 
 ARG   0.002   0.000   ARG B 548 

********************** 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
  146 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  384 MET cc_start: 0.8710 (tpp) cc_final: 0.8042 (mpp)
REVERT: A  565 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9041 (mp)
REVERT: B  378 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8482 (t0)
REVERT: B  384 MET cc_start: 0.8727 (tpp) cc_final: 0.7997 (mpp)
REVERT: B  565 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9097 (mp)
  outliers start: 32
  outliers final: 27
  residues processed: 139
  average time/residue: 0.1849
  time to fit residues: 39.2737
Evaluate side-chains
  142 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  252 SER
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  565 LEU
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  336 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  378 ASN
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  666 HIS
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 106 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 78 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 58 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:   30.0000
   chunk 5 optimal weight:    0.2980
   chunk 37 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.5984

-------------------------------------------------------------------------------
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 378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.107393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.080874 restraints weight = 24791.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.083234 restraints weight = 13474.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.084696 restraints weight = 9532.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10992  Z= 0.242
  Angle     :  0.842  59.194  14910  Z= 0.473
  Chirality :  0.038   0.142   1632
  Planarity :  0.004   0.044   1894
  Dihedral  :  3.803  15.938   1422
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.83 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.24), residues: 1300
  helix:  2.18 (0.16), residues: 942
  sheet: -1.01 (0.76), residues: 66
  loop : -1.47 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 235 
 HIS   0.003   0.001   HIS B 479 
 PHE   0.019   0.001   PHE B 335 
 TYR   0.015   0.002   TYR A  81 
 ARG   0.002   0.000   ARG A 548 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3010.38 seconds
wall clock time: 54 minutes 51.37 seconds (3291.37 seconds total)