Starting phenix.real_space_refine
on Tue Jan 14 16:47:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x5b_38065/01_2025/8x5b_38065.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x5b_38065/01_2025/8x5b_38065.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x5b_38065/01_2025/8x5b_38065.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x5b_38065/01_2025/8x5b_38065.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x5b_38065/01_2025/8x5b_38065.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x5b_38065/01_2025/8x5b_38065.cif"
  }
  resolution = 2.84
  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=   0.140
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
     P      14      5.49       5
     S      32      5.16       5
     C    4735      2.51       5
     N    1036      2.21       5
     O    1156      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6973
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "F"
      Number of atoms: 3214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3214
          Classifications: {'peptide': 393}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 378}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 52
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 46
    Chain: "A"
      Number of atoms: 3214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3214
          Classifications: {'peptide': 393}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 378}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 52
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 46
    Chain: "F"
      Number of atoms: 228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 228
          Unusual residues: {'CLR': 1, 'PO4': 4, 'POV': 8}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 236
          Unresolved non-hydrogen angles: 284
          Unresolved non-hydrogen dihedrals: 213
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 4, 'POV:plan-1': 5}
          Unresolved non-hydrogen planarities: 43
    Chain: "A"
      Number of atoms: 303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 303
          Unusual residues: {'CLR': 1, 'PO4': 4, 'POV': 10}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 265
          Unresolved non-hydrogen angles: 319
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 5}
          Unresolved non-hydrogen planarities: 41
    Chain: "F"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 4.99, per 1000 atoms: 0.72
  Number of scatterers: 6973
  At special positions: 0
  Unit cell: (75.65, 123.25, 76.5, 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)
     S      32     16.00
     P      14     15.00
     O    1156      8.00
     N    1036      7.00
     C    4735      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: 1.99
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      76.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'F' and resid 230 through 258
    Processing helix  chain 'F' and resid 265 through 296
      removed outlier: 4.602A  pdb=" N   GLY F 274 " --> pdb=" O   ARG F 270 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   GLY F 275 " --> pdb=" O   ILE F 271 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 298 through 303
    Processing helix  chain 'F' and resid 312 through 336
      removed outlier: 3.734A  pdb=" N   LEU F 316 " --> pdb=" O   SER F 312 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 345 through 361
      removed outlier: 3.898A  pdb=" N   LEU F 349 " --> pdb=" O   TYR F 345 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 367 through 383
    Processing helix  chain 'F' and resid 390 through 403
      removed outlier: 3.604A  pdb=" N   SER F 402 " --> pdb=" O   ASP F 398 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 403 through 420
      removed outlier: 4.104A  pdb=" N   LEU F 407 " --> pdb=" O   LEU F 403 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   SER F 418 " --> pdb=" O   ILE F 414 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 446 through 453
      removed outlier: 3.763A  pdb=" N   ILE F 450 " --> pdb=" O   GLY F 446 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 453 through 471
    Processing helix  chain 'F' and resid 472 through 502
      removed outlier: 4.133A  pdb=" N   HIS F 476 " --> pdb=" O   ARG F 472 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   VAL F 478 " --> pdb=" O   PHE F 474 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA F 480 " --> pdb=" O   HIS F 476 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY F 481 " --> pdb=" O   LEU F 477 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   THR F 486 " --> pdb=" O   LYS F 482 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   PHE F 487 " --> pdb=" O   TYR F 483 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   PHE F 488 " --> pdb=" O   SER F 484 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ALA F 493 " --> pdb=" O   MET F 489 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ALA F 494 " --> pdb=" O   VAL F 490 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU F 495 " --> pdb=" O   THR F 491 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 506 through 533
      removed outlier: 3.949A  pdb=" N   VAL F 516 " --> pdb=" O   TYR F 512 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 555 through 581
      removed outlier: 4.170A  pdb=" N   TYR F 559 " --> pdb=" O   GLN F 555 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE F 571 " --> pdb=" O   VAL F 567 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA F 572 " --> pdb=" O   ILE F 568 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   THR F 574 " --> pdb=" O   ARG F 570 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ILE F 575 " --> pdb=" O   PHE F 571 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN F 576 " --> pdb=" O   ALA F 572 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   SER F 581 " --> pdb=" O   ILE F 577 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 589 through 617
      Proline residue:  F 598  - end of helix
      removed outlier: 4.085A  pdb=" N   PHE F 609 " --> pdb=" O   PHE F 605 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   PHE F 610 " --> pdb=" O   VAL F 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 258
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 4.778A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 312 through 336
      removed outlier: 3.707A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 361
      removed outlier: 3.877A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 390 through 403
      removed outlier: 3.602A  pdb=" N   SER A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 420
      removed outlier: 4.104A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER A 418 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 453
      removed outlier: 4.250A  pdb=" N   ILE A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 471
    Processing helix  chain 'A' and resid 472 through 502
      removed outlier: 4.169A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   VAL A 478 " --> pdb=" O   PHE A 474 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A 481 " --> pdb=" O   LEU A 477 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   THR A 498 " --> pdb=" O   ALA A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 533
      removed outlier: 3.552A  pdb=" N   ILE A 515 " --> pdb=" O   PHE A 511 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR A 518 " --> pdb=" O   TRP A 514 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   SER A 521 " --> pdb=" O   PHE A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 580
      removed outlier: 4.170A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   THR A 574 " --> pdb=" O   ARG A 570 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLN A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER A 578 " --> pdb=" O   THR A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 617
      removed outlier: 3.551A  pdb=" N   GLY A 589 " --> pdb=" O   LEU A 585 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   ILE A 591 " --> pdb=" O   HIS A 587 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ILE A 592 " --> pdb=" O   SER A 588 " (cutoff:3.500A)
      Proline residue:  A 598  - end of helix
      removed outlier: 4.085A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)

    427 hydrogen bonds defined for protein.
    1281 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.66

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 941
        1.30 -     1.43: 2101
        1.43 -     1.56: 4045
        1.56 -     1.68: 22
        1.68 -     1.81: 44
  Bond restraints: 7153
  Sorted by residual:
  bond pdb=" O2  PO4 A 701 "
       pdb=" P   PO4 A 701 "
    ideal  model  delta    sigma   weight residual
    1.567  1.277  0.290 2.00e-02 2.50e+03 2.11e+02
  bond pdb=" C31 POV A 714 "
       pdb=" O32 POV A 714 "
    ideal  model  delta    sigma   weight residual
    1.206  1.398 -0.192 2.00e-02 2.50e+03 9.18e+01
  bond pdb=" C31 POV F 709 "
       pdb=" O32 POV F 709 "
    ideal  model  delta    sigma   weight residual
    1.206  1.398 -0.192 2.00e-02 2.50e+03 9.17e+01
  bond pdb=" C29 POV A 711 "
       pdb="C210 POV A 711 "
    ideal  model  delta    sigma   weight residual
    1.333  1.525 -0.192 2.00e-02 2.50e+03 9.17e+01
  bond pdb=" C31 POV F 712 "
       pdb=" O32 POV F 712 "
    ideal  model  delta    sigma   weight residual
    1.206  1.397 -0.191 2.00e-02 2.50e+03 9.16e+01
  ... (remaining 7148 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.06: 9434
        5.06 -    10.13: 183
       10.13 -    15.19: 27
       15.19 -    20.26: 8
       20.26 -    25.32: 3
  Bond angle restraints: 9655
  Sorted by residual:
  angle pdb=" C   TYR A 445 "
        pdb=" CA  TYR A 445 "
        pdb=" CB  TYR A 445 "
      ideal   model   delta    sigma   weight residual
     110.81   85.49   25.32 1.73e+00 3.34e-01 2.14e+02
  angle pdb=" C   LEU F 585 "
        pdb=" CA  LEU F 585 "
        pdb=" CB  LEU F 585 "
      ideal   model   delta    sigma   weight residual
     109.37  126.85  -17.48 1.59e+00 3.96e-01 1.21e+02
  angle pdb=" C   LEU A 585 "
        pdb=" N   PRO A 586 "
        pdb=" CA  PRO A 586 "
      ideal   model   delta    sigma   weight residual
     119.84  133.41  -13.57 1.25e+00 6.40e-01 1.18e+02
  angle pdb=" C   LEU F 585 "
        pdb=" N   PRO F 586 "
        pdb=" CA  PRO F 586 "
      ideal   model   delta    sigma   weight residual
     119.32  131.20  -11.88 1.14e+00 7.69e-01 1.09e+02
  angle pdb=" N   LEU F 585 "
        pdb=" CA  LEU F 585 "
        pdb=" C   LEU F 585 "
      ideal   model   delta    sigma   weight residual
     110.36   97.30   13.06 1.34e+00 5.57e-01 9.50e+01
  ... (remaining 9650 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.73: 3998
       32.73 -    65.46: 183
       65.46 -    98.18: 15
       98.18 -   130.91: 3
      130.91 -   163.64: 4
  Dihedral angle restraints: 4203
    sinusoidal: 1891
      harmonic: 2312
  Sorted by residual:
  dihedral pdb=" C   TYR A 445 "
           pdb=" N   TYR A 445 "
           pdb=" CA  TYR A 445 "
           pdb=" CB  TYR A 445 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -94.75  -27.85     0      2.50e+00 1.60e-01 1.24e+02
  dihedral pdb=" C   THR F 582 "
           pdb=" N   THR F 582 "
           pdb=" CA  THR F 582 "
           pdb=" CB  THR F 582 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -139.56   17.56     0      2.50e+00 1.60e-01 4.94e+01
  dihedral pdb=" N   THR F 582 "
           pdb=" C   THR F 582 "
           pdb=" CA  THR F 582 "
           pdb=" CB  THR F 582 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  140.71  -17.31     0      2.50e+00 1.60e-01 4.79e+01
  ... (remaining 4200 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.149: 924
       0.149 -    0.298: 77
       0.298 -    0.447: 22
       0.447 -    0.596: 3
       0.596 -    0.745: 4
  Chirality restraints: 1030
  Sorted by residual:
  chirality pdb=" CA  THR F 582 "
            pdb=" N   THR F 582 "
            pdb=" C   THR F 582 "
            pdb=" CB  THR F 582 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.78    0.74 2.00e-01 2.50e+01 1.39e+01
  chirality pdb=" CA  CYS A 620 "
            pdb=" N   CYS A 620 "
            pdb=" C   CYS A 620 "
            pdb=" CB  CYS A 620 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.89    0.62 2.00e-01 2.50e+01 9.54e+00
  chirality pdb=" CA  THR A 582 "
            pdb=" N   THR A 582 "
            pdb=" C   THR A 582 "
            pdb=" CB  THR A 582 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.91    0.61 2.00e-01 2.50e+01 9.42e+00
  ... (remaining 1027 not shown)

  Planarity restraints: 1130
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV A 711 "    0.148 2.00e-02 2.50e+03   3.46e-01 1.20e+03
        pdb=" C29 POV A 711 "   -0.446 2.00e-02 2.50e+03
        pdb="C210 POV A 711 "    0.475 2.00e-02 2.50e+03
        pdb="C211 POV A 711 "   -0.177 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV F 708 "   -0.156 2.00e-02 2.50e+03   3.23e-01 1.04e+03
        pdb=" C29 POV F 708 "    0.419 2.00e-02 2.50e+03
        pdb="C210 POV F 708 "   -0.433 2.00e-02 2.50e+03
        pdb="C211 POV F 708 "    0.170 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV F 713 "   -0.133 2.00e-02 2.50e+03   1.98e-01 3.92e+02
        pdb=" C29 POV F 713 "    0.248 2.00e-02 2.50e+03
        pdb="C210 POV F 713 "   -0.246 2.00e-02 2.50e+03
        pdb="C211 POV F 713 "    0.131 2.00e-02 2.50e+03
  ... (remaining 1127 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1621
        2.78 -     3.31: 6266
        3.31 -     3.84: 10766
        3.84 -     4.37: 13405
        4.37 -     4.90: 22962
  Nonbonded interactions: 55020
  Sorted by model distance:
  nonbonded pdb=" O3  PO4 A 701 "
            pdb=" O   HOH A 801 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O3  PO4 F 701 "
            pdb=" O   HOH F 801 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" NE2 GLN A 452 "
            pdb=" OG  SER A 581 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" O   ASN A 306 "
            pdb=" ND2 ASN A 310 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   ASN F 619 "
            pdb=" OD1 ASN F 619 "
     model   vdw
     2.333 3.040
  ... (remaining 55015 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 229 through 626 or resid 701 through 705 or (resid 706 and \ 
 (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 
27 or name C28)) or (resid 707 and (name C1 or name C2 or name C3 or name C31 or \ 
 name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 
8 or name C39 or name O11 or name O31 or name O32)) or (resid 708 and (name C21  \ 
or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name  \ 
C28 or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 o \ 
r name C213 or name C214 or name C215 or name C216)) or (resid 712 and (name C31 \ 
 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ 
 C38 or name C39 or name O31 or name O32 or name C310 or name C311 or name C312) \ 
)))
  selection = (chain 'F' and (resid 229 through 626 or resid 701 through 704 or (resid 705 and \ 
 (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 \ 
 or name C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name  \ 
C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or n \ 
ame C39 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22  \ 
or name O31 or name O32 or name P or name C210 or name C211 or name C212 or name \ 
 C213 or name C214 or name C215 or name C216 or name C217 or name C218)) or (res \ 
id 706 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ 
 or name C27 or name C28)) or (resid 707 and (name C1 or name C2 or name C3 or n \ 
ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37  \ 
or name C38 or name C39 or name O11 or name O31 or name O32)) or resid 708 or re \ 
sid 712))
}

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=0.45 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:             3.840
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.620
  Find NCS groups from input model:        0.330
  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:12.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
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      :  0.014   0.290   7153  Z= 0.848
  Angle     :  1.745  25.320   9655  Z= 0.957
  Chirality :  0.106   0.745   1030
  Planarity :  0.018   0.346   1130
  Dihedral  : 18.033 163.637   2711
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.11 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.13 %
    Favored  : 86.23 %
  Cbeta Deviations :  1.34 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -1.37 (0.26), residues: 778
  helix: -0.19 (0.20), residues: 560
  sheet:  None (None), residues: 0
  loop : -2.64 (0.31), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 514 
 HIS   0.005   0.002   HIS A 313 
 PHE   0.022   0.003   PHE A 416 
 TYR   0.022   0.002   TYR F 524 
 ARG   0.006   0.001   ARG F 459 

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

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

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.690 
Fit side-chains
REVERT: F  388 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7618 (tptp)
REVERT: F  519 ILE cc_start: 0.8581 (tt) cc_final: 0.8360 (tp)
REVERT: F  565 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8518 (tm-30)
REVERT: F  576 GLN cc_start: 0.8568 (pt0) cc_final: 0.8363 (tm-30)
REVERT: A  388 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7587 (tptp)
REVERT: A  439 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6552 (tp)
REVERT: A  565 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8524 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 115
  average time/residue: 1.2906
  time to fit residues: 156.7466
Evaluate side-chains
  78 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  440 CYS
Chi-restraints excluded: chain F residue  577 ILE
Chi-restraints excluded: chain F residue  580 THR
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  580 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 59 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0370
   chunk 20 optimal weight:    0.0070
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    0.1980
   chunk 61 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.3276

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

Flipped N/Q/H residues before XYZ refinement:
F 248 ASN
F 313 HIS
F 401 ASN
F 441 HIS
F 476 HIS
F 587 HIS
A 313 HIS
A 476 HIS
A 587 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.186772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.155187 restraints weight = 7033.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 1.45
r_work: 0.3708 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3592 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3522
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3522 r_free = 0.3522    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3518 r_free = 0.3518    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3518
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7153  Z= 0.162
  Angle     :  0.539   6.029   9655  Z= 0.291
  Chirality :  0.038   0.155   1030
  Planarity :  0.005   0.068   1130
  Dihedral  : 16.255 121.097   1330
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.62 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.03 (0.29), residues: 778
  helix:  1.67 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop : -2.33 (0.32), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 266 
 HIS   0.004   0.001   HIS A 499 
 PHE   0.015   0.001   PHE A 610 
 TYR   0.011   0.002   TYR F 352 
 ARG   0.002   0.000   ARG F 468 

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

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

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.707 
Fit side-chains
REVERT: F  515 ILE cc_start: 0.7085 (OUTLIER) cc_final: 0.6594 (tp)
REVERT: F  519 ILE cc_start: 0.8333 (tt) cc_final: 0.8124 (tp)
  outliers start: 17
  outliers final: 2
  residues processed: 86
  average time/residue: 1.0571
  time to fit residues: 96.9872
Evaluate side-chains
  63 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  515 ILE
Chi-restraints excluded: chain F residue  577 ILE
Chi-restraints excluded: chain A residue  577 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0000
   chunk 62 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.5984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.188515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.155889 restraints weight = 7181.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 1.42
r_work: 0.3611 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3478
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3478
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7153  Z= 0.164
  Angle     :  0.506   6.171   9655  Z= 0.275
  Chirality :  0.038   0.131   1030
  Planarity :  0.004   0.059   1130
  Dihedral  : 14.743 105.774   1323
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 13.32 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.66 (0.29), residues: 778
  helix:  2.16 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -2.24 (0.31), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 514 
 HIS   0.003   0.001   HIS A 313 
 PHE   0.014   0.001   PHE A 610 
 TYR   0.013   0.002   TYR F 367 
 ARG   0.002   0.000   ARG A 459 

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

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

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.713 
Fit side-chains
REVERT: F  515 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6419 (tt)
REVERT: F  519 ILE cc_start: 0.8430 (tt) cc_final: 0.8228 (tp)
REVERT: A  439 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6437 (tp)
REVERT: A  592 ILE cc_start: 0.7424 (mp) cc_final: 0.7198 (mt)
  outliers start: 14
  outliers final: 1
  residues processed: 66
  average time/residue: 1.1612
  time to fit residues: 82.0874
Evaluate side-chains
  58 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  515 ILE
Chi-restraints excluded: chain F residue  577 ILE
Chi-restraints excluded: chain A residue  439 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0070
   overall best weight:    0.6000

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.189368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.155000 restraints weight = 7199.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 1.52
r_work: 0.3585 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3447 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3453
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3453
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7153  Z= 0.155
  Angle     :  0.481   6.353   9655  Z= 0.261
  Chirality :  0.037   0.142   1030
  Planarity :  0.004   0.055   1130
  Dihedral  : 13.870 103.689   1323
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.62 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.95 (0.29), residues: 778
  helix:  2.33 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -2.01 (0.32), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 607 
 HIS   0.003   0.001   HIS A 313 
 PHE   0.013   0.001   PHE A 610 
 TYR   0.013   0.002   TYR A 352 
 ARG   0.002   0.000   ARG A 371 

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

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

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.668 
Fit side-chains
REVERT: F  515 ILE cc_start: 0.7122 (OUTLIER) cc_final: 0.6409 (tt)
REVERT: A  439 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6303 (tp)
  outliers start: 17
  outliers final: 6
  residues processed: 68
  average time/residue: 0.9352
  time to fit residues: 68.5429
Evaluate side-chains
  60 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  418 SER
Chi-restraints excluded: chain F residue  504 HIS
Chi-restraints excluded: chain F residue  515 ILE
Chi-restraints excluded: chain F residue  577 ILE
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  577 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 19 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
A 608 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.169897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.134084 restraints weight = 7163.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.58
r_work: 0.3353 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.3084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7153  Z= 0.353
  Angle     :  0.663   7.607   9655  Z= 0.352
  Chirality :  0.045   0.172   1030
  Planarity :  0.005   0.056   1130
  Dihedral  : 15.267 107.691   1323
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 14.97 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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 (0.28), residues: 778
  helix:  1.81 (0.21), residues: 580
  sheet:  None (None), residues: 0
  loop : -2.07 (0.33), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 607 
 HIS   0.006   0.001   HIS A 616 
 PHE   0.021   0.002   PHE A 605 
 TYR   0.019   0.003   TYR A 352 
 ARG   0.006   0.001   ARG F 459 

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

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

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.659 
Fit side-chains
REVERT: F  306 ASN cc_start: 0.8046 (t0) cc_final: 0.7676 (t0)
REVERT: F  422 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6781 (pttp)
REVERT: F  515 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6529 (tt)
REVERT: A  422 LYS cc_start: 0.7397 (ptmt) cc_final: 0.6759 (pttp)
REVERT: A  439 ILE cc_start: 0.6983 (OUTLIER) cc_final: 0.6557 (tp)
  outliers start: 17
  outliers final: 7
  residues processed: 67
  average time/residue: 1.2078
  time to fit residues: 85.8671
Evaluate side-chains
  61 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  398 ASP
Chi-restraints excluded: chain F residue  418 SER
Chi-restraints excluded: chain F residue  422 LYS
Chi-restraints excluded: chain F residue  515 ILE
Chi-restraints excluded: chain F residue  577 ILE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  577 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.0870
   chunk 10 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.7362

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

Flipped N/Q/H residues before XYZ refinement:
F 248 ASN
F 288 ASN
F 540 ASN
A 248 ASN
A 288 ASN
A 540 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.184767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.154069 restraints weight = 7133.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 1.32
r_work: 0.3565 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3430
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3430
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7153  Z= 0.174
  Angle     :  0.499   6.537   9655  Z= 0.272
  Chirality :  0.038   0.139   1030
  Planarity :  0.004   0.053   1130
  Dihedral  : 14.122 101.558   1323
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.47 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.87 (0.29), residues: 778
  helix:  2.24 (0.20), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.90 (0.34), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 607 
 HIS   0.003   0.001   HIS A 313 
 PHE   0.012   0.001   PHE F 610 
 TYR   0.013   0.002   TYR A 352 
 ARG   0.002   0.000   ARG A 371 

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

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

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.750 
Fit side-chains
REVERT: F  515 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6463 (tt)
REVERT: A  439 ILE cc_start: 0.6870 (OUTLIER) cc_final: 0.6442 (tp)
  outliers start: 12
  outliers final: 4
  residues processed: 59
  average time/residue: 1.0558
  time to fit residues: 67.0176
Evaluate side-chains
  56 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  418 SER
Chi-restraints excluded: chain F residue  515 ILE
Chi-restraints excluded: chain F residue  577 ILE
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  504 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 67 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
F 288 ASN
A 288 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.184457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.151297 restraints weight = 7054.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 1.42
r_work: 0.3556 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3422 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3429
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3428
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7153  Z= 0.178
  Angle     :  0.500   6.457   9655  Z= 0.272
  Chirality :  0.038   0.140   1030
  Planarity :  0.004   0.051   1130
  Dihedral  : 13.808  99.561   1323
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 16.02 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.29), residues: 778
  helix:  2.34 (0.20), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.77 (0.35), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 514 
 HIS   0.003   0.001   HIS A 313 
 PHE   0.012   0.001   PHE F 610 
 TYR   0.011   0.002   TYR A 367 
 ARG   0.002   0.000   ARG A 371 

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

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

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A  439 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6337 (tp)
  outliers start: 16
  outliers final: 7
  residues processed: 59
  average time/residue: 1.0464
  time to fit residues: 66.2443
Evaluate side-chains
  56 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  398 ASP
Chi-restraints excluded: chain F residue  418 SER
Chi-restraints excluded: chain F residue  504 HIS
Chi-restraints excluded: chain F residue  577 ILE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  504 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 59 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
F 288 ASN
A 288 ASN
A 452 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.182231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.148647 restraints weight = 7121.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 1.43
r_work: 0.3529 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7153  Z= 0.209
  Angle     :  0.529   6.775   9655  Z= 0.288
  Chirality :  0.039   0.143   1030
  Planarity :  0.004   0.051   1130
  Dihedral  : 13.911  98.347   1323
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.17 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.96 (0.29), residues: 778
  helix:  2.27 (0.20), residues: 580
  sheet:  None (None), residues: 0
  loop : -1.79 (0.36), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP F 607 
 HIS   0.004   0.001   HIS A 313 
 PHE   0.013   0.001   PHE F 605 
 TYR   0.013   0.002   TYR A 367 
 ARG   0.002   0.000   ARG A 371 

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

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

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.739 
Fit side-chains
REVERT: F  306 ASN cc_start: 0.8204 (t0) cc_final: 0.7891 (t0)
REVERT: A  439 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6346 (tp)
  outliers start: 15
  outliers final: 5
  residues processed: 60
  average time/residue: 1.0636
  time to fit residues: 68.8742
Evaluate side-chains
  54 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  418 SER
Chi-restraints excluded: chain F residue  504 HIS
Chi-restraints excluded: chain F residue  577 ILE
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  439 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
F 288 ASN
A 288 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.184853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.153882 restraints weight = 7188.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 1.32
r_work: 0.3561 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3436
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3436
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7153  Z= 0.180
  Angle     :  0.499   6.451   9655  Z= 0.273
  Chirality :  0.038   0.140   1030
  Planarity :  0.004   0.050   1130
  Dihedral  : 13.513  94.489   1323
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.32 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.29), residues: 778
  helix:  2.36 (0.20), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.73 (0.36), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP F 514 
 HIS   0.003   0.001   HIS A 313 
 PHE   0.012   0.001   PHE F 517 
 TYR   0.011   0.002   TYR A 352 
 ARG   0.002   0.000   ARG F 371 

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

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

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.688 
Fit side-chains
REVERT: F  515 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6433 (tt)
REVERT: A  439 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6334 (tp)
  outliers start: 13
  outliers final: 5
  residues processed: 59
  average time/residue: 1.0007
  time to fit residues: 63.6578
Evaluate side-chains
  54 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  418 SER
Chi-restraints excluded: chain F residue  504 HIS
Chi-restraints excluded: chain F residue  515 ILE
Chi-restraints excluded: chain F residue  577 ILE
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  504 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
F 288 ASN
A 288 ASN
A 452 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.180109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.145084 restraints weight = 7252.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 1.52
r_work: 0.3464 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3332
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3332
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   7153  Z= 0.294
  Angle     :  0.604   7.300   9655  Z= 0.324
  Chirality :  0.043   0.150   1030
  Planarity :  0.005   0.052   1130
  Dihedral  : 14.187  96.651   1323
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.62 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.67 (0.29), residues: 778
  helix:  2.04 (0.20), residues: 580
  sheet:  None (None), residues: 0
  loop : -1.86 (0.36), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP F 607 
 HIS   0.005   0.001   HIS A 313 
 PHE   0.019   0.002   PHE F 605 
 TYR   0.015   0.002   TYR A 367 
 ARG   0.004   0.001   ARG F 459 

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

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

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1556 Ramachandran restraints generated.
    778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.679 
Fit side-chains
REVERT: F  306 ASN cc_start: 0.8221 (t0) cc_final: 0.7801 (t0)
REVERT: F  515 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.6511 (tt)
REVERT: A  439 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6436 (tp)
  outliers start: 11
  outliers final: 5
  residues processed: 60
  average time/residue: 1.1269
  time to fit residues: 72.0050
Evaluate side-chains
  56 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  418 SER
Chi-restraints excluded: chain F residue  504 HIS
Chi-restraints excluded: chain F residue  515 ILE
Chi-restraints excluded: chain F residue  577 ILE
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  504 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 59 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0170
   chunk 41 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
F 248 ASN
F 288 ASN
A 248 ASN
A 288 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.185929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.152504 restraints weight = 7075.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 1.43
r_work: 0.3572 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3440
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3440
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7153  Z= 0.166
  Angle     :  0.492   6.399   9655  Z= 0.268
  Chirality :  0.037   0.139   1030
  Planarity :  0.004   0.050   1130
  Dihedral  : 13.437  88.189   1323
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 17.07 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.29), residues: 778
  helix:  2.35 (0.20), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.76 (0.36), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 607 
 HIS   0.003   0.001   HIS F 616 
 PHE   0.012   0.001   PHE A 610 
 TYR   0.010   0.001   TYR F 553 
 ARG   0.002   0.000   ARG F 371 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4656.89 seconds
wall clock time: 84 minutes 7.23 seconds (5047.23 seconds total)