Starting phenix.real_space_refine
on Tue Jul 29 02:26:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xk0_38412/07_2025/8xk0_38412.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xk0_38412/07_2025/8xk0_38412.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xk0_38412/07_2025/8xk0_38412.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xk0_38412/07_2025/8xk0_38412.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xk0_38412/07_2025/8xk0_38412.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xk0_38412/07_2025/8xk0_38412.cif"
  }
  resolution = 2.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.072
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5720 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     P      32      5.49       5
     S      29      5.16       5
     C    3910      2.51       5
     N    1116      2.21       5
     O    1213      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6302
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 692, 5621
          Classifications: {'peptide': 692}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 23, 'TRANS': 668}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 359
          Classifications: {'DNA': 17}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 16}
    Chain: "C"
      Number of atoms: 298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 298
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2, 'water': 17}
          Link IDs: {None: 18}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.46, per 1000 atoms: 0.71
  Number of scatterers: 6302
  At special positions: 0
  Unit cell: (74.888, 91.057, 111.481, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      2     24.99
     S      29     16.00
     P      32     15.00
     O    1213      8.00
     N    1116      7.00
     C    3910      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 895.9 milliseconds
  

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1320

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 8 sheets defined
      36.6% alpha, 19.9% beta
      7 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 2.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 17
      No H-bonds generated for 'chain 'A' and resid 15 through 17'
    Processing helix  chain 'A' and resid 36 through 48
    Processing helix  chain 'A' and resid 84 through 105
    Processing helix  chain 'A' and resid 160 through 165
      removed outlier: 3.748A  pdb=" N   GLU A 165 " --> pdb=" O   GLN A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 269
    Processing helix  chain 'A' and resid 271 through 290
      removed outlier: 3.777A  pdb=" N   TRP A 282 " --> pdb=" O   CYS A 278 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE A 283 " --> pdb=" O   THR A 279 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA A 288 " --> pdb=" O   GLN A 284 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLN A 289 " --> pdb=" O   GLN A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 332
    Processing helix  chain 'A' and resid 349 through 354
    Processing helix  chain 'A' and resid 358 through 375
      removed outlier: 3.508A  pdb=" N   VAL A 368 " --> pdb=" O   GLN A 364 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA A 375 " --> pdb=" O   LYS A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 388
    Processing helix  chain 'A' and resid 394 through 400
    Processing helix  chain 'A' and resid 400 through 405
    Processing helix  chain 'A' and resid 406 through 412
      removed outlier: 3.807A  pdb=" N   GLN A 409 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      Proline residue:  A 410  - end of helix
      No H-bonds generated for 'chain 'A' and resid 406 through 412'
    Processing helix  chain 'A' and resid 422 through 428
    Processing helix  chain 'A' and resid 432 through 442
    Processing helix  chain 'A' and resid 453 through 467
      removed outlier: 3.916A  pdb=" N   ILE A 457 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 477
      removed outlier: 3.516A  pdb=" N   GLU A 477 " --> pdb=" O   PRO A 474 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 474 through 477'
    Processing helix  chain 'A' and resid 478 through 488
      removed outlier: 3.841A  pdb=" N   ARG A 482 " --> pdb=" O   GLN A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 507
    Processing helix  chain 'A' and resid 565 through 583
      removed outlier: 3.544A  pdb=" N   GLN A 583 " --> pdb=" O   ALA A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 613
      removed outlier: 3.920A  pdb=" N   VAL A 606 " --> pdb=" O   HIS A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 692
    Processing helix  chain 'A' and resid 706 through 721
      removed outlier: 3.839A  pdb=" N   ALA A 712 " --> pdb=" O   THR A 708 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU A 714 " --> pdb=" O   HIS A 710 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   SER A 715 " --> pdb=" O   TYR A 711 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5
    Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13
      removed outlier: 5.251A  pdb=" N   ILE A 144 " --> pdb=" O   SER A  10 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   VAL A 127 " --> pdb=" O   GLN A 122 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   GLN A 122 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   ILE A 129 " --> pdb=" O   GLN A 120 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   GLN A 120 " --> pdb=" O   ILE A 129 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLU A 131 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 53
    Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178
    Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 234
      removed outlier: 3.653A  pdb=" N   ILE A 231 " --> pdb=" O   TYR A 242 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TYR A 242 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 311
      removed outlier: 3.700A  pdb=" N   THR A 646 " --> pdb=" O   CYS A 657 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ILE A 591 " --> pdb=" O   ASP A 618 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   VAL A 620 " --> pdb=" O   ILE A 591 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   ILE A 593 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ILE A 622 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ARG A 595 " --> pdb=" O   ILE A 622 " (cutoff:3.500A)
      removed outlier: 5.561A  pdb=" N   VAL A 528 " --> pdb=" O   ASP A 596 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323
    Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 382
      removed outlier: 8.748A  pdb=" N   THR A 416 " --> pdb=" O   ASN A 340 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LYS A 342 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   LEU A 418 " --> pdb=" O   LYS A 342 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   SER A 344 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   PHE A 420 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A 346 " --> pdb=" O   PHE A 420 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   VAL A 417 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   ILE A 452 " --> pdb=" O   VAL A 417 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ALA A 419 " --> pdb=" O   ILE A 452 " (cutoff:3.500A)

    229 hydrogen bonds defined for protein.
    645 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      17 hydrogen bonds
      34 hydrogen bond angles
      0 basepair planarities
      7 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 2.27 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1568
        1.33 -     1.45: 1391
        1.45 -     1.57: 3414
        1.57 -     1.69: 63
        1.69 -     1.81: 51
  Bond restraints: 6487
  Sorted by residual:
  bond pdb=" P    DT B   1 "
       pdb=" OP3  DT B   1 "
    ideal  model  delta    sigma   weight residual
    1.480  1.592 -0.112 2.00e-02 2.50e+03 3.16e+01
  bond pdb=" O3'  DT B   1 "
       pdb=" P    DG B   2 "
    ideal  model  delta    sigma   weight residual
    1.607  1.574  0.033 1.50e-02 4.44e+03 4.71e+00
  bond pdb=" P    DA B  17 "
       pdb=" OP2  DA B  17 "
    ideal  model  delta    sigma   weight residual
    1.480  1.517 -0.037 2.00e-02 2.50e+03 3.35e+00
  bond pdb=" P    DT B  16 "
       pdb=" OP1  DT B  16 "
    ideal  model  delta    sigma   weight residual
    1.480  1.515 -0.035 2.00e-02 2.50e+03 3.13e+00
  bond pdb=" P    DA B  17 "
       pdb=" OP1  DA B  17 "
    ideal  model  delta    sigma   weight residual
    1.480  1.515 -0.035 2.00e-02 2.50e+03 3.00e+00
  ... (remaining 6482 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 8663
        1.54 -     3.08: 206
        3.08 -     4.61: 29
        4.61 -     6.15: 8
        6.15 -     7.69: 5
  Bond angle restraints: 8911
  Sorted by residual:
  angle pdb=" N   PRO A 474 "
        pdb=" CA  PRO A 474 "
        pdb=" CB  PRO A 474 "
      ideal   model   delta    sigma   weight residual
     103.25  110.94   -7.69 1.05e+00 9.07e-01 5.37e+01
  angle pdb=" N   VAL A 542 "
        pdb=" CA  VAL A 542 "
        pdb=" C   VAL A 542 "
      ideal   model   delta    sigma   weight residual
     109.34  103.16    6.18 2.08e+00 2.31e-01 8.84e+00
  angle pdb=" C   TYR A 473 "
        pdb=" N   PRO A 474 "
        pdb=" CA  PRO A 474 "
      ideal   model   delta    sigma   weight residual
     119.84  123.27   -3.43 1.25e+00 6.40e-01 7.51e+00
  angle pdb=" C   GLN A 731 "
        pdb=" N   THR A 732 "
        pdb=" CA  THR A 732 "
      ideal   model   delta    sigma   weight residual
     121.54  126.60   -5.06 1.91e+00 2.74e-01 7.01e+00
  angle pdb=" C4   DT B  16 "
        pdb=" C5   DT B  16 "
        pdb=" C7   DT B  16 "
      ideal   model   delta    sigma   weight residual
     122.40  118.49    3.91 1.50e+00 4.44e-01 6.79e+00
  ... (remaining 8906 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.50: 3625
       32.50 -    65.00: 155
       65.00 -    97.50: 11
       97.50 -   130.00: 0
      130.00 -   162.50: 1
  Dihedral angle restraints: 3792
    sinusoidal: 1750
      harmonic: 2042
  Sorted by residual:
  dihedral pdb=" C4'  DT B  16 "
           pdb=" C3'  DT B  16 "
           pdb=" O3'  DT B  16 "
           pdb=" P    DA B  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   57.50  162.50     1      3.50e+01 8.16e-04 1.53e+01
  dihedral pdb=" N   PRO A 474 "
           pdb=" C   PRO A 474 "
           pdb=" CA  PRO A 474 "
           pdb=" CB  PRO A 474 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  123.91   -8.81     0      2.50e+00 1.60e-01 1.24e+01
  dihedral pdb=" CA  ASN A 541 "
           pdb=" C   ASN A 541 "
           pdb=" N   VAL A 542 "
           pdb=" CA  VAL A 542 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.29   15.71     0      5.00e+00 4.00e-02 9.88e+00
  ... (remaining 3789 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.116: 977
       0.116 -    0.232: 14
       0.232 -    0.348: 1
       0.348 -    0.465: 0
       0.465 -    0.581: 2
  Chirality restraints: 994
  Sorted by residual:
  chirality pdb=" P    DA B  17 "
            pdb=" OP1  DA B  17 "
            pdb=" OP2  DA B  17 "
            pdb=" O5'  DA B  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.93   -0.58 2.00e-01 2.50e+01 8.43e+00
  chirality pdb=" P    DT B  16 "
            pdb=" OP1  DT B  16 "
            pdb=" OP2  DT B  16 "
            pdb=" O5'  DT B  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.85   -0.50 2.00e-01 2.50e+01 6.27e+00
  chirality pdb=" CA  PRO A 474 "
            pdb=" N   PRO A 474 "
            pdb=" C   PRO A 474 "
            pdb=" CB  PRO A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.60e+00
  ... (remaining 991 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 553 "   -0.043 5.00e-02 4.00e+02   6.50e-02 6.75e+00
        pdb=" N   PRO A 554 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 554 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 554 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 583 "    0.007 2.00e-02 2.50e+03   1.39e-02 1.92e+00
        pdb=" C   GLN A 583 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   GLN A 583 "    0.009 2.00e-02 2.50e+03
        pdb=" N   PHE A 584 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT B   1 "    0.017 2.00e-02 2.50e+03   8.52e-03 1.82e+00
        pdb=" N1   DT B   1 "   -0.018 2.00e-02 2.50e+03
        pdb=" C2   DT B   1 "    0.002 2.00e-02 2.50e+03
        pdb=" O2   DT B   1 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3   DT B   1 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DT B   1 "    0.002 2.00e-02 2.50e+03
        pdb=" O4   DT B   1 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DT B   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" C7   DT B   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DT B   1 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 43
        2.60 -     3.17: 4972
        3.17 -     3.75: 9288
        3.75 -     4.32: 13839
        4.32 -     4.90: 22613
  Nonbonded interactions: 50755
  Sorted by model distance:
  nonbonded pdb=" OP1  DT C   7 "
            pdb="MN    MN A 802 "
     model   vdw
     2.023 2.320
  nonbonded pdb=" OP1  DA B   3 "
            pdb="MN    MN A 801 "
     model   vdw
     2.128 2.320
  nonbonded pdb=" O   GLN A 669 "
            pdb=" O   HOH A 901 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OP3  DT B   1 "
            pdb="MN    MN A 801 "
     model   vdw
     2.238 2.320
  nonbonded pdb=" OD1 ASP A  48 "
            pdb=" NH2 ARG A 105 "
     model   vdw
     2.273 3.120
  ... (remaining 50750 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
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:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     21.460
  Find NCS groups from input model:        0.070
  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:             0.010
  Load rotamer database and sin/cos tables:13.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
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      :  0.003   0.112   6487  Z= 0.155
  Angle     :  0.595   7.691   8911  Z= 0.327
  Chirality :  0.049   0.581    994
  Planarity :  0.004   0.065   1020
  Dihedral  : 16.436 162.500   2472
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  6.27 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.00 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.69 (0.32), residues: 686
  helix:  0.65 (0.35), residues: 234
  sheet: -0.11 (0.41), residues: 162
  loop : -1.56 (0.34), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 445 
 HIS   0.007   0.001   HIS A 465 
 PHE   0.019   0.001   PHE A 682 
 TYR   0.020   0.001   TYR A 719 
 ARG   0.002   0.000   ARG A 600 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18410 (  246)
  hydrogen bonds       : angle       5.86853 (  679)
  covalent geometry    : bond        0.00324 ( 6487)
  covalent geometry    : angle       0.59503 ( 8911)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.610 
Fit side-chains
REVERT: A  108 HIS cc_start: 0.6966 (m-70) cc_final: 0.6764 (m90)
  outliers start: 1
  outliers final: 1
  residues processed: 104
  average time/residue: 1.1782
  time to fit residues: 128.9344
Evaluate side-chains
  90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 180 ASN
A 259 GLN
A 465 HIS
A 467 HIS
A 701 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.157392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.119886 restraints weight = 7255.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.92
r_work: 0.3126 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6487  Z= 0.221
  Angle     :  0.650   9.704   8911  Z= 0.352
  Chirality :  0.045   0.165    994
  Planarity :  0.004   0.042   1020
  Dihedral  : 15.861 148.618   1111
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  6.41 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.67 %
    Favored  : 87.85 %
  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: -0.86 (0.32), residues: 686
  helix:  0.51 (0.35), residues: 237
  sheet: -0.16 (0.41), residues: 161
  loop : -1.70 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 512 
 HIS   0.007   0.001   HIS A 320 
 PHE   0.024   0.002   PHE A 319 
 TYR   0.014   0.002   TYR A 130 
 ARG   0.008   0.001   ARG A 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05309 (  246)
  hydrogen bonds       : angle       4.79281 (  679)
  covalent geometry    : bond        0.00516 ( 6487)
  covalent geometry    : angle       0.65050 ( 8911)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  108 HIS cc_start: 0.7631 (m-70) cc_final: 0.7395 (m90)
REVERT: A  435 GLN cc_start: 0.8219 (tt0) cc_final: 0.7856 (tp-100)
  outliers start: 9
  outliers final: 2
  residues processed: 100
  average time/residue: 1.0080
  time to fit residues: 107.2097
Evaluate side-chains
  85 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  128 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    0.4980
   chunk 58 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.158940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.122177 restraints weight = 7285.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.84
r_work: 0.3189 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6487  Z= 0.142
  Angle     :  0.569   8.115   8911  Z= 0.311
  Chirality :  0.042   0.173    994
  Planarity :  0.004   0.037   1020
  Dihedral  : 15.496 144.756   1109
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.98 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.97 %
    Favored  : 85.39 %
  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: -0.61 (0.32), residues: 686
  helix:  0.79 (0.35), residues: 234
  sheet:  0.18 (0.43), residues: 146
  loop : -1.67 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 599 
 HIS   0.008   0.001   HIS A 320 
 PHE   0.022   0.002   PHE A 319 
 TYR   0.010   0.001   TYR A 719 
 ARG   0.006   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03992 (  246)
  hydrogen bonds       : angle       4.47800 (  679)
  covalent geometry    : bond        0.00318 ( 6487)
  covalent geometry    : angle       0.56885 ( 8911)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 HIS cc_start: 0.7498 (m-70) cc_final: 0.7272 (m90)
REVERT: A  435 GLN cc_start: 0.8196 (tt0) cc_final: 0.7817 (tp-100)
  outliers start: 10
  outliers final: 4
  residues processed: 95
  average time/residue: 1.3347
  time to fit residues: 134.9762
Evaluate side-chains
  87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   73 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  572 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 425 HIS
A 467 HIS
A 552 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.156314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.119740 restraints weight = 7184.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.88
r_work: 0.3143 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.054   6487  Z= 0.366
  Angle     :  0.753   9.646   8911  Z= 0.408
  Chirality :  0.051   0.168    994
  Planarity :  0.005   0.042   1020
  Dihedral  : 16.245 146.309   1109
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  6.41 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.26 %
    Favored  : 80.95 %
  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: -1.17 (0.31), residues: 686
  helix:  0.10 (0.34), residues: 238
  sheet: -0.02 (0.41), residues: 161
  loop : -1.96 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 512 
 HIS   0.008   0.001   HIS A 320 
 PHE   0.029   0.003   PHE A 351 
 TYR   0.017   0.002   TYR A 130 
 ARG   0.007   0.001   ARG A  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06323 (  246)
  hydrogen bonds       : angle       5.08948 (  679)
  covalent geometry    : bond        0.00871 ( 6487)
  covalent geometry    : angle       0.75349 ( 8911)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 HIS cc_start: 0.7815 (m-70) cc_final: 0.7610 (m90)
REVERT: A  371 LYS cc_start: 0.8916 (tptt) cc_final: 0.8573 (tptp)
REVERT: A  428 ASN cc_start: 0.7271 (t0) cc_final: 0.6986 (t0)
REVERT: A  435 GLN cc_start: 0.8345 (tt0) cc_final: 0.7928 (tp-100)
REVERT: A  578 LYS cc_start: 0.8203 (mmmm) cc_final: 0.7997 (mmtp)
  outliers start: 17
  outliers final: 8
  residues processed: 99
  average time/residue: 0.9805
  time to fit residues: 103.5265
Evaluate side-chains
  90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  701 ASN
Chi-restraints excluded: chain A residue  737 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 178 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.163119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.126635 restraints weight = 7140.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.72
r_work: 0.3265 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6487  Z= 0.135
  Angle     :  0.572   9.330   8911  Z= 0.312
  Chirality :  0.042   0.174    994
  Planarity :  0.004   0.039   1020
  Dihedral  : 15.532 144.172   1109
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.54 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.06 %
    Favored  : 79.97 %
  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: -0.76 (0.32), residues: 686
  helix:  0.63 (0.35), residues: 236
  sheet:  0.34 (0.43), residues: 140
  loop : -1.86 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 599 
 HIS   0.008   0.001   HIS A 320 
 PHE   0.022   0.001   PHE A 319 
 TYR   0.010   0.001   TYR A 719 
 ARG   0.006   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03822 (  246)
  hydrogen bonds       : angle       4.55315 (  679)
  covalent geometry    : bond        0.00300 ( 6487)
  covalent geometry    : angle       0.57218 ( 8911)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
REVERT: A  435 GLN cc_start: 0.8199 (tt0) cc_final: 0.7842 (tp-100)
  outliers start: 12
  outliers final: 5
  residues processed: 95
  average time/residue: 0.9362
  time to fit residues: 94.9460
Evaluate side-chains
  86 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   73 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  572 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 60 optimal weight:    0.2980
   chunk 70 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 178 HIS
A 364 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.160425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.122080 restraints weight = 7073.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.98
r_work: 0.3182 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6487  Z= 0.213
  Angle     :  0.631   8.958   8911  Z= 0.344
  Chirality :  0.045   0.164    994
  Planarity :  0.004   0.041   1020
  Dihedral  : 15.779 143.664   1109
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.98 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.41 %
    Favored  : 79.31 %
  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: -0.85 (0.32), residues: 686
  helix:  0.50 (0.35), residues: 238
  sheet:  0.38 (0.44), residues: 145
  loop : -1.95 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 512 
 HIS   0.008   0.001   HIS A 320 
 PHE   0.023   0.002   PHE A 319 
 TYR   0.013   0.001   TYR A 130 
 ARG   0.007   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04763 (  246)
  hydrogen bonds       : angle       4.69496 (  679)
  covalent geometry    : bond        0.00500 ( 6487)
  covalent geometry    : angle       0.63139 ( 8911)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A  435 GLN cc_start: 0.8249 (tt0) cc_final: 0.7844 (tp-100)
REVERT: A  562 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6438 (mm-30)
  outliers start: 20
  outliers final: 12
  residues processed: 95
  average time/residue: 0.9732
  time to fit residues: 98.3742
Evaluate side-chains
  91 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   73 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  134 GLU
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  737 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 178 HIS
A 467 HIS
A 701 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.163457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.125851 restraints weight = 7169.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.76
r_work: 0.3230 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6487  Z= 0.134
  Angle     :  0.581   9.068   8911  Z= 0.314
  Chirality :  0.042   0.170    994
  Planarity :  0.003   0.039   1020
  Dihedral  : 15.491 141.940   1109
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.10 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 17.73 %
    Favored  : 78.82 %
  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: -0.56 (0.32), residues: 686
  helix:  0.82 (0.35), residues: 234
  sheet:  0.34 (0.43), residues: 151
  loop : -1.74 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 599 
 HIS   0.008   0.001   HIS A 320 
 PHE   0.021   0.001   PHE A 319 
 TYR   0.012   0.001   TYR A 719 
 ARG   0.006   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  246)
  hydrogen bonds       : angle       4.46744 (  679)
  covalent geometry    : bond        0.00302 ( 6487)
  covalent geometry    : angle       0.58067 ( 8911)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8876 (m-80)
REVERT: A  435 GLN cc_start: 0.8184 (tt0) cc_final: 0.7787 (tp-100)
  outliers start: 21
  outliers final: 6
  residues processed: 100
  average time/residue: 0.9068
  time to fit residues: 96.6623
Evaluate side-chains
  89 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   73 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0170
   chunk 65 optimal weight:    4.9990
   chunk 25 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    0.6622

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.164977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.129844 restraints weight = 7057.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.56
r_work: 0.3277 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6487  Z= 0.126
  Angle     :  0.572   8.814   8911  Z= 0.310
  Chirality :  0.042   0.166    994
  Planarity :  0.003   0.038   1020
  Dihedral  : 15.372 139.809   1109
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.54 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 20.20 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.50 (0.32), residues: 686
  helix:  0.97 (0.35), residues: 234
  sheet:  0.33 (0.43), residues: 146
  loop : -1.74 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 599 
 HIS   0.008   0.001   HIS A 320 
 PHE   0.020   0.001   PHE A 319 
 TYR   0.014   0.001   TYR A 719 
 ARG   0.007   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03468 (  246)
  hydrogen bonds       : angle       4.39746 (  679)
  covalent geometry    : bond        0.00281 ( 6487)
  covalent geometry    : angle       0.57199 ( 8911)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8845 (m-80)
REVERT: A  435 GLN cc_start: 0.8053 (tt0) cc_final: 0.7733 (tp-100)
  outliers start: 11
  outliers final: 7
  residues processed: 93
  average time/residue: 0.9933
  time to fit residues: 98.4582
Evaluate side-chains
  91 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  134 GLU
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  427 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.161450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.124952 restraints weight = 7131.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.69
r_work: 0.3242 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6487  Z= 0.202
  Angle     :  0.625   8.149   8911  Z= 0.338
  Chirality :  0.045   0.166    994
  Planarity :  0.004   0.040   1020
  Dihedral  : 15.674 140.131   1109
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.54 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.70 %
    Favored  : 78.16 %
  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: -0.74 (0.32), residues: 686
  helix:  0.70 (0.35), residues: 239
  sheet:  0.14 (0.42), residues: 155
  loop : -1.88 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 512 
 HIS   0.008   0.001   HIS A 320 
 PHE   0.023   0.002   PHE A 319 
 TYR   0.015   0.002   TYR A 719 
 ARG   0.007   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04558 (  246)
  hydrogen bonds       : angle       4.63547 (  679)
  covalent geometry    : bond        0.00472 ( 6487)
  covalent geometry    : angle       0.62466 ( 8911)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
REVERT: A  435 GLN cc_start: 0.8083 (tt0) cc_final: 0.7761 (tp-100)
  outliers start: 13
  outliers final: 9
  residues processed: 90
  average time/residue: 1.0153
  time to fit residues: 97.0502
Evaluate side-chains
  91 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  134 GLU
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  572 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 8 optimal weight:    0.4980
   chunk 53 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 43 optimal weight:    0.2980
   chunk 52 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.164844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.127834 restraints weight = 7184.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.72
r_work: 0.3273 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6487  Z= 0.127
  Angle     :  0.580   9.612   8911  Z= 0.313
  Chirality :  0.043   0.171    994
  Planarity :  0.003   0.038   1020
  Dihedral  : 15.378 138.148   1109
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.25 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 20.20 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.54 (0.32), residues: 686
  helix:  0.88 (0.35), residues: 236
  sheet:  0.33 (0.42), residues: 153
  loop : -1.79 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 599 
 HIS   0.008   0.001   HIS A 320 
 PHE   0.020   0.001   PHE A 319 
 TYR   0.014   0.001   TYR A 719 
 ARG   0.007   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03469 (  246)
  hydrogen bonds       : angle       4.44902 (  679)
  covalent geometry    : bond        0.00283 ( 6487)
  covalent geometry    : angle       0.58009 ( 8911)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
REVERT: A  435 GLN cc_start: 0.8021 (tt0) cc_final: 0.7695 (tp-100)
  outliers start: 11
  outliers final: 6
  residues processed: 95
  average time/residue: 0.9866
  time to fit residues: 99.4340
Evaluate side-chains
  94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.163925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.127673 restraints weight = 7309.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 1.69
r_work: 0.3276 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6487  Z= 0.145
  Angle     :  0.591   9.408   8911  Z= 0.318
  Chirality :  0.043   0.185    994
  Planarity :  0.004   0.063   1020
  Dihedral  : 15.419 136.630   1109
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.54 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 20.69 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.55 (0.32), residues: 686
  helix:  0.84 (0.35), residues: 236
  sheet:  0.28 (0.42), residues: 155
  loop : -1.75 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 599 
 HIS   0.008   0.001   HIS A 320 
 PHE   0.020   0.002   PHE A 319 
 TYR   0.015   0.001   TYR A 719 
 ARG   0.014   0.000   ARG A 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03785 (  246)
  hydrogen bonds       : angle       4.45510 (  679)
  covalent geometry    : bond        0.00332 ( 6487)
  covalent geometry    : angle       0.59090 ( 8911)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4735.36 seconds
wall clock time: 81 minutes 55.66 seconds (4915.66 seconds total)