Starting phenix.real_space_refine
on Wed Sep 17 18:53:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xry_38611/09_2025/8xry_38611.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xry_38611/09_2025/8xry_38611.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xry_38611/09_2025/8xry_38611.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xry_38611/09_2025/8xry_38611.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xry_38611/09_2025/8xry_38611.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xry_38611/09_2025/8xry_38611.map"
  }
  resolution = 3.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.071
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    7032      2.51       5
     N    1722      2.21       5
     O    1826      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10616
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 696, 5308
          Classifications: {'peptide': 696}
          Incomplete info: {'truncation_to_alanine': 68}
          Link IDs: {'PTRANS': 31, 'TRANS': 664}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 270
          Unresolved non-hydrogen angles: 333
          Unresolved non-hydrogen dihedrals: 224
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 5, 'TRP:plan': 1, 'GLU:plan': 15, 'ASP:plan': 3, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 167
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.06, per 1000 atoms: 0.38
  Number of scatterers: 10616
  At special positions: 0
  Unit cell: (90.73, 139.26, 102.335, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1826      8.00
     N    1722      7.00
     C    7032      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 395.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2664

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 2 sheets defined
      72.0% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 29
      removed outlier: 4.217A  pdb=" N   ARG A  29 " --> pdb=" O   THR A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 32
      No H-bonds generated for 'chain 'A' and resid 30 through 32'
    Processing helix  chain 'A' and resid 33 through 38
    Processing helix  chain 'A' and resid 61 through 67
    Processing helix  chain 'A' and resid 69 through 77
    Processing helix  chain 'A' and resid 78 through 100
      removed outlier: 3.658A  pdb=" N   ALA A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 112
      removed outlier: 4.395A  pdb=" N   THR A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   LEU A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      Proline residue:  A 108  - end of helix
    Processing helix  chain 'A' and resid 117 through 121
    Processing helix  chain 'A' and resid 134 through 139
      removed outlier: 3.567A  pdb=" N   MET A 139 " --> pdb=" O   ASP A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 184
      removed outlier: 3.764A  pdb=" N   GLY A 154 " --> pdb=" O   TRP A 150 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   ALA A 155 " --> pdb=" O   ALA A 151 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   TRP A 158 " --> pdb=" O   GLY A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 218
    Processing helix  chain 'A' and resid 233 through 254
    Processing helix  chain 'A' and resid 265 through 269
    Processing helix  chain 'A' and resid 273 through 277
    Processing helix  chain 'A' and resid 279 through 303
      removed outlier: 3.845A  pdb=" N   TYR A 283 " --> pdb=" O   ASP A 279 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU A 287 " --> pdb=" O   TYR A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 325
    Processing helix  chain 'A' and resid 355 through 376
    Processing helix  chain 'A' and resid 377 through 386
      removed outlier: 4.017A  pdb=" N   ILE A 381 " --> pdb=" O   TYR A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 391
    Processing helix  chain 'A' and resid 392 through 396
    Processing helix  chain 'A' and resid 401 through 409
      removed outlier: 3.570A  pdb=" N   ALA A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ILE A 409 " --> pdb=" O   GLU A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 439
      Proline residue:  A 418  - end of helix
      removed outlier: 4.069A  pdb=" N   PHE A 425 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 444 through 469
      removed outlier: 4.039A  pdb=" N   ILE A 466 " --> pdb=" O   PHE A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 484
    Processing helix  chain 'A' and resid 486 through 498
      removed outlier: 3.690A  pdb=" N   ILE A 490 " --> pdb=" O   LYS A 486 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 501
      No H-bonds generated for 'chain 'A' and resid 499 through 501'
    Processing helix  chain 'A' and resid 502 through 523
    Processing helix  chain 'A' and resid 523 through 536
    Processing helix  chain 'A' and resid 540 through 546
    Processing helix  chain 'A' and resid 557 through 572
    Processing helix  chain 'A' and resid 578 through 601
      removed outlier: 3.967A  pdb=" N   PHE A 582 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 610
      removed outlier: 4.224A  pdb=" N   GLY A 610 " --> pdb=" O   GLU A 607 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 607 through 610'
    Processing helix  chain 'A' and resid 611 through 638
      removed outlier: 4.508A  pdb=" N   HIS A 615 " --> pdb=" O   ARG A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 665
      removed outlier: 3.558A  pdb=" N   VAL A 646 " --> pdb=" O   TYR A 642 " (cutoff:3.500A)
      Proline residue:  A 648  - end of helix
    Processing helix  chain 'A' and resid 665 through 670
      removed outlier: 3.725A  pdb=" N   GLU A 669 " --> pdb=" O   TYR A 665 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   HIS A 670 " --> pdb=" O   GLY A 666 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 665 through 670'
    Processing helix  chain 'A' and resid 686 through 694
      removed outlier: 4.105A  pdb=" N   PHE A 690 " --> pdb=" O   LEU A 686 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 29
      removed outlier: 4.217A  pdb=" N   ARG B  29 " --> pdb=" O   THR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 32
      No H-bonds generated for 'chain 'B' and resid 30 through 32'
    Processing helix  chain 'B' and resid 33 through 38
    Processing helix  chain 'B' and resid 61 through 67
    Processing helix  chain 'B' and resid 69 through 77
    Processing helix  chain 'B' and resid 78 through 100
      removed outlier: 3.658A  pdb=" N   ALA B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 112
      removed outlier: 4.394A  pdb=" N   THR B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   LEU B 107 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      Proline residue:  B 108  - end of helix
    Processing helix  chain 'B' and resid 117 through 121
    Processing helix  chain 'B' and resid 134 through 139
      removed outlier: 3.568A  pdb=" N   MET B 139 " --> pdb=" O   ASP B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 184
      removed outlier: 3.764A  pdb=" N   GLY B 154 " --> pdb=" O   TRP B 150 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   ALA B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TRP B 158 " --> pdb=" O   GLY B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 218
    Processing helix  chain 'B' and resid 233 through 254
    Processing helix  chain 'B' and resid 265 through 269
    Processing helix  chain 'B' and resid 273 through 277
    Processing helix  chain 'B' and resid 279 through 303
      removed outlier: 3.846A  pdb=" N   TYR B 283 " --> pdb=" O   ASP B 279 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LEU B 287 " --> pdb=" O   TYR B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 325
    Processing helix  chain 'B' and resid 355 through 376
    Processing helix  chain 'B' and resid 377 through 386
      removed outlier: 4.018A  pdb=" N   ILE B 381 " --> pdb=" O   TYR B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 391
    Processing helix  chain 'B' and resid 392 through 396
    Processing helix  chain 'B' and resid 401 through 409
      removed outlier: 3.570A  pdb=" N   ALA B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ILE B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 439
      Proline residue:  B 418  - end of helix
      removed outlier: 4.070A  pdb=" N   PHE B 425 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
      Proline residue:  B 430  - end of helix
    Processing helix  chain 'B' and resid 444 through 469
      removed outlier: 4.039A  pdb=" N   ILE B 466 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 484
    Processing helix  chain 'B' and resid 486 through 498
      removed outlier: 3.690A  pdb=" N   ILE B 490 " --> pdb=" O   LYS B 486 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU B 498 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 501
      No H-bonds generated for 'chain 'B' and resid 499 through 501'
    Processing helix  chain 'B' and resid 502 through 523
    Processing helix  chain 'B' and resid 523 through 536
    Processing helix  chain 'B' and resid 540 through 546
    Processing helix  chain 'B' and resid 557 through 572
    Processing helix  chain 'B' and resid 578 through 601
      removed outlier: 3.967A  pdb=" N   PHE B 582 " --> pdb=" O   LEU B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 610
      removed outlier: 4.224A  pdb=" N   GLY B 610 " --> pdb=" O   GLU B 607 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 607 through 610'
    Processing helix  chain 'B' and resid 611 through 638
      removed outlier: 4.509A  pdb=" N   HIS B 615 " --> pdb=" O   ARG B 611 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 642 through 665
      removed outlier: 3.558A  pdb=" N   VAL B 646 " --> pdb=" O   TYR B 642 " (cutoff:3.500A)
      Proline residue:  B 648  - end of helix
    Processing helix  chain 'B' and resid 665 through 670
      removed outlier: 3.726A  pdb=" N   GLU B 669 " --> pdb=" O   TYR B 665 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   HIS B 670 " --> pdb=" O   GLY B 666 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 665 through 670'
    Processing helix  chain 'B' and resid 686 through 694
      removed outlier: 4.105A  pdb=" N   PHE B 690 " --> pdb=" O   LEU B 686 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229
    Processing sheet with id=AA2, first strand: chain 'B' and resid 228 through 229

    672 hydrogen bonds defined for protein.
    1944 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: 1.45

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3211
        1.34 -     1.46: 2241
        1.46 -     1.58: 5382
        1.58 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 10892
  Sorted by residual:
  bond pdb=" C   LEU B 498 "
       pdb=" N   PRO B 499 "
    ideal  model  delta    sigma   weight residual
    1.334  1.348 -0.014 8.40e-03 1.42e+04 2.87e+00
  bond pdb=" C   LEU A 498 "
       pdb=" N   PRO A 499 "
    ideal  model  delta    sigma   weight residual
    1.334  1.347 -0.013 8.40e-03 1.42e+04 2.52e+00
  bond pdb=" C   ILE B 397 "
       pdb=" N   PRO B 398 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 2.34e-02 1.83e+03 1.22e+00
  bond pdb=" C   ILE A 397 "
       pdb=" N   PRO A 398 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.17e+00
  bond pdb=" CA  GLN A 206 "
       pdb=" C   GLN A 206 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.012 1.34e-02 5.57e+03 8.41e-01
  ... (remaining 10887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 14549
        2.11 -     4.22: 247
        4.22 -     6.33: 58
        6.33 -     8.45: 8
        8.45 -    10.56: 6
  Bond angle restraints: 14868
  Sorted by residual:
  angle pdb=" C   PRO A 203 "
        pdb=" N   ASP A 204 "
        pdb=" CA  ASP A 204 "
      ideal   model   delta    sigma   weight residual
     121.54  128.50   -6.96 1.91e+00 2.74e-01 1.33e+01
  angle pdb=" C   PRO B 203 "
        pdb=" N   ASP B 204 "
        pdb=" CA  ASP B 204 "
      ideal   model   delta    sigma   weight residual
     121.54  128.47   -6.93 1.91e+00 2.74e-01 1.32e+01
  angle pdb=" C   PRO A  58 "
        pdb=" N   PHE A  59 "
        pdb=" CA  PHE A  59 "
      ideal   model   delta    sigma   weight residual
     121.54  128.33   -6.79 1.91e+00 2.74e-01 1.27e+01
  angle pdb=" C   PRO B  58 "
        pdb=" N   PHE B  59 "
        pdb=" CA  PHE B  59 "
      ideal   model   delta    sigma   weight residual
     121.54  128.29   -6.75 1.91e+00 2.74e-01 1.25e+01
  angle pdb=" C   LYS B 486 "
        pdb=" N   LEU B 487 "
        pdb=" CA  LEU B 487 "
      ideal   model   delta    sigma   weight residual
     121.54  127.64   -6.10 1.91e+00 2.74e-01 1.02e+01
  ... (remaining 14863 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.33: 5710
       16.33 -    32.66: 558
       32.66 -    48.98: 90
       48.98 -    65.31: 16
       65.31 -    81.64: 2
  Dihedral angle restraints: 6376
    sinusoidal: 2270
      harmonic: 4106
  Sorted by residual:
  dihedral pdb=" CA  PHE A  59 "
           pdb=" C   PHE A  59 "
           pdb=" N   ALA A  60 "
           pdb=" CA  ALA A  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.92   33.08     0      5.00e+00 4.00e-02 4.38e+01
  dihedral pdb=" CA  PHE B  59 "
           pdb=" C   PHE B  59 "
           pdb=" N   ALA B  60 "
           pdb=" CA  ALA B  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.95   33.05     0      5.00e+00 4.00e-02 4.37e+01
  dihedral pdb=" CA  GLY B 441 "
           pdb=" C   GLY B 441 "
           pdb=" N   ILE B 442 "
           pdb=" CA  ILE B 442 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.20   28.80     0      5.00e+00 4.00e-02 3.32e+01
  ... (remaining 6373 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1162
       0.037 -    0.074: 441
       0.074 -    0.111: 140
       0.111 -    0.148: 27
       0.148 -    0.185: 6
  Chirality restraints: 1776
  Sorted by residual:
  chirality pdb=" CA  ASP A 204 "
            pdb=" N   ASP A 204 "
            pdb=" C   ASP A 204 "
            pdb=" CB  ASP A 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.55e-01
  chirality pdb=" CA  ASP B 204 "
            pdb=" N   ASP B 204 "
            pdb=" C   ASP B 204 "
            pdb=" CB  ASP B 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" CA  PHE A 664 "
            pdb=" N   PHE A 664 "
            pdb=" C   PHE A 664 "
            pdb=" CB  PHE A 664 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.15e-01
  ... (remaining 1773 not shown)

  Planarity restraints: 1826
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 202 "    0.046 5.00e-02 4.00e+02   7.01e-02 7.86e+00
        pdb=" N   PRO A 203 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 203 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 203 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 202 "   -0.046 5.00e-02 4.00e+02   6.97e-02 7.77e+00
        pdb=" N   PRO B 203 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO B 203 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 203 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 484 "    0.046 5.00e-02 4.00e+02   6.89e-02 7.60e+00
        pdb=" N   PRO A 485 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 485 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 485 "    0.038 5.00e-02 4.00e+02
  ... (remaining 1823 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2534
        2.78 -     3.31: 10899
        3.31 -     3.84: 17498
        3.84 -     4.37: 18819
        4.37 -     4.90: 32469
  Nonbonded interactions: 82219
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  56 "
            pdb=" O   ALA A  60 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" NH2 ARG B  56 "
            pdb=" O   ALA B  60 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" ND2 ASN A 261 "
            pdb=" OG  SER A 280 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" OD1 ASP A 562 "
            pdb=" OH  TYR A 586 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OD1 ASP B 562 "
            pdb=" OH  TYR B 586 "
     model   vdw
     2.300 3.040
  ... (remaining 82214 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.970
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
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      :  0.004   0.028  10892  Z= 0.165
  Angle     :  0.744  10.558  14868  Z= 0.395
  Chirality :  0.044   0.185   1776
  Planarity :  0.005   0.070   1826
  Dihedral  : 12.985  81.641   3712
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.32 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.24), residues: 1384
  helix:  0.98 (0.18), residues: 904
  sheet:  None (None), residues: 0
  loop : -2.50 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 359 
 TYR   0.024   0.002   TYR B 171 
 PHE   0.018   0.002   PHE B 376 
 TRP   0.011   0.001   TRP A 613 
 HIS   0.005   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10892)
  covalent geometry    : angle       0.74391 (14868)
  hydrogen bonds       : bond        0.13394 (  672)
  hydrogen bonds       : angle       5.16342 ( 1944)

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A  240 TRP cc_start: 0.9092 (t60) cc_final: 0.8641 (t60)
REVERT: A  462 PHE cc_start: 0.7374 (m-10) cc_final: 0.7127 (m-10)
REVERT: A  522 SER cc_start: 0.9371 (p) cc_final: 0.9118 (p)
REVERT: B   14 PHE cc_start: 0.8836 (t80) cc_final: 0.8592 (t80)
REVERT: B   26 TRP cc_start: 0.8555 (t60) cc_final: 0.8331 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0674
  time to fit residues: 18.6070
Evaluate side-chains
  139 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0010
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.0870
   chunk 103 optimal weight:    0.0670
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.2902

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

Flipped N/Q/H residues before XYZ refinement:
A 353 ASN
B 353 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.167357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.122851 restraints weight = 15071.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.123843 restraints weight = 15792.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.123702 restraints weight = 11889.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.123682 restraints weight = 9445.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.123781 restraints weight = 9250.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10892  Z= 0.133
  Angle     :  0.679  12.685  14868  Z= 0.336
  Chirality :  0.042   0.161   1776
  Planarity :  0.005   0.062   1826
  Dihedral  :  5.160  31.877   1484
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 10.24 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.24), residues: 1384
  helix:  1.04 (0.18), residues: 912
  sheet:  None (None), residues: 0
  loop : -2.63 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 450 
 TYR   0.018   0.001   TYR B 693 
 PHE   0.039   0.002   PHE B 640 
 TRP   0.008   0.001   TRP A 613 
 HIS   0.005   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10892)
  covalent geometry    : angle       0.67917 (14868)
  hydrogen bonds       : bond        0.04160 (  672)
  hydrogen bonds       : angle       4.35896 ( 1944)

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 174
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A  113 ASP cc_start: 0.7587 (p0) cc_final: 0.7173 (p0)
REVERT: A  240 TRP cc_start: 0.8991 (t60) cc_final: 0.8639 (t60)
REVERT: A  522 SER cc_start: 0.9307 (p) cc_final: 0.9073 (p)
REVERT: A  642 TYR cc_start: 0.6759 (p90) cc_final: 0.6390 (p90)
REVERT: B   14 PHE cc_start: 0.8841 (t80) cc_final: 0.8611 (t80)
REVERT: B  113 ASP cc_start: 0.7490 (p0) cc_final: 0.7100 (p0)
REVERT: B  522 SER cc_start: 0.9365 (p) cc_final: 0.9156 (p)
REVERT: B  690 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7186 (m-10)
  outliers start: 18
  outliers final: 11
  residues processed: 184
  average time/residue: 0.0740
  time to fit residues: 21.2638
Evaluate side-chains
  161 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  690 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 134 optimal weight:    0.6980
   chunk 19 optimal weight:    0.1980
   chunk 126 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 107 optimal weight:   20.0000
   chunk 112 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 261 ASN
** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.158552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.113198 restraints weight = 15359.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.112598 restraints weight = 17426.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.113440 restraints weight = 15790.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.113352 restraints weight = 12061.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.113440 restraints weight = 10989.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10892  Z= 0.129
  Angle     :  0.647  11.427  14868  Z= 0.318
  Chirality :  0.042   0.170   1776
  Planarity :  0.005   0.064   1826
  Dihedral  :  4.959  30.880   1484
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.99 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.24), residues: 1384
  helix:  1.08 (0.18), residues: 916
  sheet: -2.07 (1.14), residues: 20
  loop : -2.63 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 611 
 TYR   0.023   0.001   TYR B 171 
 PHE   0.027   0.001   PHE B 513 
 TRP   0.009   0.001   TRP B  61 
 HIS   0.002   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10892)
  covalent geometry    : angle       0.64724 (14868)
  hydrogen bonds       : bond        0.03900 (  672)
  hydrogen bonds       : angle       4.21923 ( 1944)

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 159
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.7611 (p0) cc_final: 0.7158 (p0)
REVERT: A  240 TRP cc_start: 0.9065 (t60) cc_final: 0.8566 (t60)
REVERT: A  522 SER cc_start: 0.9405 (p) cc_final: 0.9188 (p)
REVERT: A  642 TYR cc_start: 0.6637 (p90) cc_final: 0.6320 (p90)
REVERT: B   14 PHE cc_start: 0.8927 (t80) cc_final: 0.8691 (t80)
REVERT: B  113 ASP cc_start: 0.7734 (p0) cc_final: 0.7260 (p0)
REVERT: B  423 ILE cc_start: 0.8642 (mm) cc_final: 0.8153 (tp)
REVERT: B  690 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7048 (m-10)
  outliers start: 23
  outliers final: 12
  residues processed: 173
  average time/residue: 0.0746
  time to fit residues: 20.3249
Evaluate side-chains
  156 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  690 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 133 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0970
   chunk 86 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 90 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 615 HIS
B 670 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.164233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.120618 restraints weight = 15277.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.119823 restraints weight = 18507.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.121068 restraints weight = 16102.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.120683 restraints weight = 13018.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.120766 restraints weight = 11778.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10892  Z= 0.128
  Angle     :  0.639  10.266  14868  Z= 0.311
  Chirality :  0.042   0.188   1776
  Planarity :  0.005   0.062   1826
  Dihedral  :  4.807  31.110   1484
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.29 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.24), residues: 1384
  helix:  1.16 (0.18), residues: 914
  sheet: -1.48 (1.25), residues: 20
  loop : -2.63 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  56 
 TYR   0.024   0.001   TYR B 171 
 PHE   0.027   0.001   PHE A 513 
 TRP   0.009   0.001   TRP A 548 
 HIS   0.002   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10892)
  covalent geometry    : angle       0.63890 (14868)
  hydrogen bonds       : bond        0.03667 (  672)
  hydrogen bonds       : angle       4.10868 ( 1944)

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 159
  time to evaluate  : 0.434 
Fit side-chains
REVERT: A   29 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7749 (mtt-85)
REVERT: A  113 ASP cc_start: 0.7389 (p0) cc_final: 0.7003 (p0)
REVERT: A  240 TRP cc_start: 0.9091 (t60) cc_final: 0.8595 (t60)
REVERT: A  520 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8367 (tm-30)
REVERT: A  548 TRP cc_start: 0.8501 (p-90) cc_final: 0.8240 (p-90)
REVERT: A  642 TYR cc_start: 0.6621 (p90) cc_final: 0.6342 (p90)
REVERT: B   14 PHE cc_start: 0.8855 (t80) cc_final: 0.8617 (t80)
REVERT: B   43 LEU cc_start: 0.9152 (mt) cc_final: 0.8950 (mt)
REVERT: B  113 ASP cc_start: 0.7541 (p0) cc_final: 0.7117 (p0)
REVERT: B  690 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7088 (m-10)
  outliers start: 34
  outliers final: 19
  residues processed: 180
  average time/residue: 0.0869
  time to fit residues: 23.8612
Evaluate side-chains
  159 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  428 MET
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  690 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 125 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0170
   chunk 132 optimal weight:    0.0970
   chunk 57 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   overall best weight:    0.5616

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

Flipped N/Q/H residues before XYZ refinement:
A 670 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.166356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.121522 restraints weight = 15058.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.121896 restraints weight = 15782.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.123324 restraints weight = 12152.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.122752 restraints weight = 10729.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.122923 restraints weight = 9919.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10892  Z= 0.119
  Angle     :  0.646  12.454  14868  Z= 0.308
  Chirality :  0.041   0.166   1776
  Planarity :  0.005   0.067   1826
  Dihedral  :  4.688  30.825   1484
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.90 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.25), residues: 1384
  helix:  1.22 (0.18), residues: 918
  sheet: -1.03 (1.32), residues: 20
  loop : -2.52 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  56 
 TYR   0.021   0.001   TYR B 171 
 PHE   0.025   0.001   PHE A 513 
 TRP   0.008   0.001   TRP B 548 
 HIS   0.003   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10892)
  covalent geometry    : angle       0.64632 (14868)
  hydrogen bonds       : bond        0.03510 (  672)
  hydrogen bonds       : angle       4.06356 ( 1944)

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.7358 (p0) cc_final: 0.6967 (p0)
REVERT: A  226 ARG cc_start: 0.5797 (ptm160) cc_final: 0.5596 (ptm160)
REVERT: A  240 TRP cc_start: 0.9095 (t60) cc_final: 0.8618 (t60)
REVERT: A  571 CYS cc_start: 0.8249 (m) cc_final: 0.7365 (t)
REVERT: A  642 TYR cc_start: 0.6602 (p90) cc_final: 0.6317 (p90)
REVERT: B   14 PHE cc_start: 0.8744 (t80) cc_final: 0.8506 (t80)
REVERT: B   43 LEU cc_start: 0.9084 (mt) cc_final: 0.8875 (mt)
REVERT: B  113 ASP cc_start: 0.7535 (p0) cc_final: 0.7096 (p0)
REVERT: B  690 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7167 (m-10)
  outliers start: 31
  outliers final: 21
  residues processed: 173
  average time/residue: 0.0869
  time to fit residues: 22.6986
Evaluate side-chains
  165 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  690 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 74 optimal weight:    0.0670
   chunk 130 optimal weight:    0.5980
   chunk 94 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 97 optimal weight:   10.0000
   chunk 77 optimal weight:    0.8980
   chunk 109 optimal weight:   30.0000
   chunk 86 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
B 141 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.158665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.113042 restraints weight = 15427.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.112657 restraints weight = 17329.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.113840 restraints weight = 15317.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.113664 restraints weight = 11259.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.113816 restraints weight = 10461.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10892  Z= 0.120
  Angle     :  0.643  11.319  14868  Z= 0.305
  Chirality :  0.041   0.157   1776
  Planarity :  0.005   0.070   1826
  Dihedral  :  4.615  30.736   1484
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.81 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.25), residues: 1384
  helix:  1.28 (0.18), residues: 926
  sheet: -0.64 (1.37), residues: 20
  loop : -2.43 (0.32), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  56 
 TYR   0.025   0.001   TYR B 171 
 PHE   0.026   0.001   PHE B 664 
 TRP   0.014   0.001   TRP A 548 
 HIS   0.003   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10892)
  covalent geometry    : angle       0.64276 (14868)
  hydrogen bonds       : bond        0.03447 (  672)
  hydrogen bonds       : angle       3.98634 ( 1944)

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 148
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7320 (ttm110) cc_final: 0.7082 (ttm110)
REVERT: A  113 ASP cc_start: 0.7451 (p0) cc_final: 0.7098 (p0)
REVERT: A  240 TRP cc_start: 0.9078 (t60) cc_final: 0.8586 (t60)
REVERT: A  571 CYS cc_start: 0.8453 (m) cc_final: 0.7455 (t)
REVERT: A  642 TYR cc_start: 0.6526 (p90) cc_final: 0.6306 (p90)
REVERT: B   14 PHE cc_start: 0.8721 (t80) cc_final: 0.8496 (t80)
REVERT: B  113 ASP cc_start: 0.7553 (p0) cc_final: 0.7153 (p0)
REVERT: B  690 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7105 (m-10)
  outliers start: 38
  outliers final: 29
  residues processed: 175
  average time/residue: 0.0834
  time to fit residues: 22.4653
Evaluate side-chains
  167 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  428 MET
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  606 TYR
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  690 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0270
   chunk 26 optimal weight:   30.0000
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 132 optimal weight:    0.4980
   chunk 40 optimal weight:   20.0000
   chunk 46 optimal weight:    7.9990
   overall best weight:    0.8240

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.164412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.114396 restraints weight = 16296.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.112240 restraints weight = 13957.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.113327 restraints weight = 11794.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.114108 restraints weight = 9765.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.114184 restraints weight = 8777.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10892  Z= 0.134
  Angle     :  0.663  13.367  14868  Z= 0.313
  Chirality :  0.041   0.152   1776
  Planarity :  0.005   0.072   1826
  Dihedral  :  4.612  31.351   1484
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 20.20 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.25), residues: 1384
  helix:  1.28 (0.18), residues: 928
  sheet: -0.55 (1.35), residues: 20
  loop : -2.41 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  56 
 TYR   0.027   0.001   TYR B 171 
 PHE   0.023   0.001   PHE A 513 
 TRP   0.018   0.001   TRP A 548 
 HIS   0.003   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10892)
  covalent geometry    : angle       0.66328 (14868)
  hydrogen bonds       : bond        0.03498 (  672)
  hydrogen bonds       : angle       3.98597 ( 1944)

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 144
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7408 (ttm110) cc_final: 0.7153 (ttm110)
REVERT: A  113 ASP cc_start: 0.7654 (p0) cc_final: 0.7273 (p0)
REVERT: A  240 TRP cc_start: 0.9021 (t60) cc_final: 0.8534 (t60)
REVERT: A  642 TYR cc_start: 0.6584 (p90) cc_final: 0.6318 (p90)
REVERT: B   14 PHE cc_start: 0.8694 (t80) cc_final: 0.8485 (t80)
REVERT: B  113 ASP cc_start: 0.7740 (p0) cc_final: 0.7251 (p0)
  outliers start: 36
  outliers final: 28
  residues processed: 169
  average time/residue: 0.0890
  time to fit residues: 22.9617
Evaluate side-chains
  166 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  428 MET
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  606 TYR
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  690 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 74 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0770
   chunk 36 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9980
   chunk 124 optimal weight:    0.7980
   chunk 117 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0970
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
B 277 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.182637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.138353 restraints weight = 15681.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.137658 restraints weight = 12087.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.138689 restraints weight = 10018.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.139162 restraints weight = 8638.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.139330 restraints weight = 8232.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10892  Z= 0.113
  Angle     :  0.652  10.371  14868  Z= 0.305
  Chirality :  0.041   0.143   1776
  Planarity :  0.004   0.066   1826
  Dihedral  :  4.513  31.266   1484
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.58 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.25), residues: 1384
  helix:  1.43 (0.18), residues: 916
  sheet: -0.12 (1.40), residues: 20
  loop : -2.39 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  56 
 TYR   0.022   0.001   TYR B 171 
 PHE   0.022   0.001   PHE A 513 
 TRP   0.019   0.001   TRP A 548 
 HIS   0.003   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (10892)
  covalent geometry    : angle       0.65182 (14868)
  hydrogen bonds       : bond        0.03332 (  672)
  hydrogen bonds       : angle       3.93027 ( 1944)

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 143
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7369 (ttm110) cc_final: 0.7102 (ttm110)
REVERT: A  113 ASP cc_start: 0.7553 (p0) cc_final: 0.7210 (p0)
REVERT: A  317 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8922 (p)
REVERT: A  571 CYS cc_start: 0.8335 (m) cc_final: 0.7381 (t)
REVERT: A  642 TYR cc_start: 0.6539 (p90) cc_final: 0.6337 (p90)
REVERT: B   14 PHE cc_start: 0.8673 (t80) cc_final: 0.8466 (t80)
REVERT: B  183 MET cc_start: 0.7951 (tpp) cc_final: 0.7653 (tpp)
REVERT: B  571 CYS cc_start: 0.8092 (m) cc_final: 0.7806 (t)
  outliers start: 35
  outliers final: 25
  residues processed: 168
  average time/residue: 0.0862
  time to fit residues: 21.6820
Evaluate side-chains
  160 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  428 MET
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  525 ILE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  690 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0060
   chunk 0 optimal weight:   20.0000
   chunk 114 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 105 optimal weight:    0.8980
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.171833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.123701 restraints weight = 15967.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.122529 restraints weight = 12054.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.122747 restraints weight = 10394.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.123478 restraints weight = 9425.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.123686 restraints weight = 8621.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10892  Z= 0.124
  Angle     :  0.666  12.814  14868  Z= 0.311
  Chirality :  0.041   0.144   1776
  Planarity :  0.005   0.064   1826
  Dihedral  :  4.493  30.994   1484
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.23 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.25), residues: 1384
  helix:  1.46 (0.18), residues: 916
  sheet: -0.03 (1.40), residues: 20
  loop : -2.38 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  56 
 TYR   0.023   0.001   TYR B 171 
 PHE   0.026   0.001   PHE B 664 
 TRP   0.019   0.001   TRP A 548 
 HIS   0.002   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10892)
  covalent geometry    : angle       0.66569 (14868)
  hydrogen bonds       : bond        0.03351 (  672)
  hydrogen bonds       : angle       3.95186 ( 1944)

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7356 (ttm110) cc_final: 0.7094 (ttm110)
REVERT: A  113 ASP cc_start: 0.7628 (p0) cc_final: 0.7258 (p0)
REVERT: A  378 MET cc_start: 0.7271 (mmm) cc_final: 0.6785 (mmm)
REVERT: A  571 CYS cc_start: 0.8313 (m) cc_final: 0.7443 (t)
REVERT: A  642 TYR cc_start: 0.6539 (p90) cc_final: 0.6322 (p90)
REVERT: B   14 PHE cc_start: 0.8677 (t80) cc_final: 0.8469 (t80)
REVERT: B  183 MET cc_start: 0.7976 (tpp) cc_final: 0.7640 (tpp)
REVERT: B  579 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8294 (tt)
REVERT: B  690 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7086 (m-10)
  outliers start: 30
  outliers final: 26
  residues processed: 157
  average time/residue: 0.0920
  time to fit residues: 21.5812
Evaluate side-chains
  161 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  428 MET
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  525 ILE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  606 TYR
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  690 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 120 optimal weight:    0.8980
   chunk 121 optimal weight:    0.0000
   chunk 95 optimal weight:    8.9990
   chunk 5 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0870
   chunk 67 optimal weight:    8.9990
   chunk 108 optimal weight:   20.0000
   chunk 70 optimal weight:    3.9990
   chunk 117 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.4562

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

Flipped N/Q/H residues before XYZ refinement:
B 261 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.180134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.135878 restraints weight = 15788.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.134553 restraints weight = 11992.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.135052 restraints weight = 9575.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.135478 restraints weight = 9078.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.135707 restraints weight = 8830.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10892  Z= 0.114
  Angle     :  0.657  12.486  14868  Z= 0.306
  Chirality :  0.040   0.152   1776
  Planarity :  0.004   0.063   1826
  Dihedral  :  4.435  31.140   1484
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 21.23 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.25), residues: 1384
  helix:  1.50 (0.18), residues: 918
  sheet:  0.05 (1.40), residues: 20
  loop : -2.33 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  63 
 TYR   0.021   0.001   TYR B 171 
 PHE   0.017   0.001   PHE B 640 
 TRP   0.020   0.001   TRP B 548 
 HIS   0.002   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10892)
  covalent geometry    : angle       0.65723 (14868)
  hydrogen bonds       : bond        0.03273 (  672)
  hydrogen bonds       : angle       3.92571 ( 1944)

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7363 (ttm110) cc_final: 0.7098 (ttm110)
REVERT: A  113 ASP cc_start: 0.7508 (p0) cc_final: 0.7151 (p0)
REVERT: A  378 MET cc_start: 0.7208 (mmm) cc_final: 0.6794 (mmm)
REVERT: A  571 CYS cc_start: 0.8225 (m) cc_final: 0.7405 (t)
REVERT: A  642 TYR cc_start: 0.6455 (p90) cc_final: 0.6242 (p90)
REVERT: A  690 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7282 (m-10)
REVERT: B   14 PHE cc_start: 0.8660 (t80) cc_final: 0.8443 (t80)
REVERT: B  183 MET cc_start: 0.7921 (tpp) cc_final: 0.7583 (tpp)
REVERT: B  378 MET cc_start: 0.7570 (mmm) cc_final: 0.7092 (mmm)
REVERT: B  571 CYS cc_start: 0.8213 (m) cc_final: 0.7807 (t)
REVERT: B  579 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8262 (tt)
REVERT: B  690 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7121 (m-10)
  outliers start: 28
  outliers final: 23
  residues processed: 155
  average time/residue: 0.0839
  time to fit residues: 19.6589
Evaluate side-chains
  155 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  428 MET
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  171 TYR
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  525 ILE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  606 TYR
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  690 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 123 optimal weight:    0.0970
   chunk 71 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 132 optimal weight:    0.0980
   chunk 8 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.4027 r_free = 0.4027 target = 0.182645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.138914 restraints weight = 15754.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.138176 restraints weight = 11351.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.138518 restraints weight = 9277.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.138648 restraints weight = 8579.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.138818 restraints weight = 8354.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10892  Z= 0.118
  Angle     :  0.660  12.112  14868  Z= 0.309
  Chirality :  0.041   0.151   1776
  Planarity :  0.004   0.062   1826
  Dihedral  :  4.402  30.556   1484
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.51 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.25), residues: 1384
  helix:  1.54 (0.18), residues: 916
  sheet:  0.13 (1.40), residues: 20
  loop : -2.31 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  56 
 TYR   0.020   0.001   TYR B 171 
 PHE   0.017   0.001   PHE B 640 
 TRP   0.020   0.001   TRP A 548 
 HIS   0.002   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (10892)
  covalent geometry    : angle       0.66044 (14868)
  hydrogen bonds       : bond        0.03264 (  672)
  hydrogen bonds       : angle       3.91193 ( 1944)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1623.56 seconds
wall clock time: 28 minutes 58.47 seconds (1738.47 seconds total)