Starting phenix.real_space_refine
on Fri Feb 14 19:23:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xry_38611/02_2025/8xry_38611.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xry_38611/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xry_38611/02_2025/8xry_38611.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xry_38611/02_2025/8xry_38611.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xry_38611/02_2025/8xry_38611.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xry_38611/02_2025/8xry_38611.cif"
  }
  resolution = 3.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 167
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.86, per 1000 atoms: 0.93
  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: 2.73
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.17
  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: 2.99

  Time building geometry restraints manager: 3.11 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: 0.06
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:             0.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.480
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.720
-------------------------------------------------------------------------------
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= 0.229
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (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
 TRP   0.011   0.001   TRP A 613 
 HIS   0.005   0.001   HIS A 615 
 PHE   0.018   0.002   PHE B 376 
 TYR   0.024   0.002   TYR B 171 
 ARG   0.002   0.000   ARG A 359 

*********************** 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  : 1.214 
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: 0.1687
  time to fit residues: 45.8194
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  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    6.9990
   chunk 104 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 108 optimal weight:   30.0000
   chunk 41 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 80 optimal weight:    8.9990
   chunk 125 optimal weight:    0.3980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 353 ASN
B 261 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.163682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.123299 restraints weight = 14898.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.122091 restraints weight = 21811.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.123398 restraints weight = 19644.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10892  Z= 0.246
  Angle     :  0.697  12.060  14868  Z= 0.348
  Chirality :  0.043   0.167   1776
  Planarity :  0.005   0.063   1826
  Dihedral  :  5.239  32.015   1484
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.45 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 10.34 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.24), residues: 1384
  helix:  1.02 (0.18), residues: 912
  sheet:  None (None), residues: 0
  loop : -2.67 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 613 
 HIS   0.004   0.001   HIS A 615 
 PHE   0.037   0.002   PHE B 640 
 TYR   0.016   0.002   TYR B 171 
 ARG   0.002   0.000   ARG B 450 

*********************** 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
  184 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 163
  time to evaluate  : 1.137 
Fit side-chains
REVERT: A  113 ASP cc_start: 0.7594 (p0) cc_final: 0.7208 (p0)
REVERT: A  198 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7563 (m-30)
REVERT: A  240 TRP cc_start: 0.9049 (t60) cc_final: 0.8658 (t60)
REVERT: A  519 LEU cc_start: 0.9409 (mm) cc_final: 0.9128 (mp)
REVERT: A  522 SER cc_start: 0.9333 (p) cc_final: 0.9072 (p)
REVERT: A  642 TYR cc_start: 0.6792 (p90) cc_final: 0.6354 (p90)
REVERT: B   14 PHE cc_start: 0.8759 (t80) cc_final: 0.8527 (t80)
REVERT: B  113 ASP cc_start: 0.7480 (p0) cc_final: 0.7172 (p0)
REVERT: B  522 SER cc_start: 0.9393 (p) cc_final: 0.9186 (p)
REVERT: B  690 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7269 (m-10)
  outliers start: 21
  outliers final: 14
  residues processed: 174
  average time/residue: 0.1694
  time to fit residues: 46.0906
Evaluate side-chains
  159 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 1.400 
-------------------------------------------------------------------------------
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  198 ASP
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  506 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  601 VAL
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 44 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 66 optimal weight:    0.2980
   chunk 113 optimal weight:    0.8980
   chunk 98 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 123 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 96 optimal weight:    6.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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**
B 353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.157606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.113957 restraints weight = 15528.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.112172 restraints weight = 20100.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.113523 restraints weight = 18729.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1534

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= 0.197
  Angle     :  0.649  10.770  14868  Z= 0.320
  Chirality :  0.042   0.138   1776
  Planarity :  0.005   0.063   1826
  Dihedral  :  5.043  31.510   1484
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 14.80 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.24), residues: 1384
  helix:  1.06 (0.18), residues: 916
  sheet: -2.15 (1.14), residues: 20
  loop : -2.60 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  61 
 HIS   0.005   0.001   HIS A 615 
 PHE   0.028   0.001   PHE B 513 
 TYR   0.030   0.001   TYR B 171 
 ARG   0.002   0.000   ARG B 197 

*********************** 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
  191 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.7509 (p0) cc_final: 0.7088 (p0)
REVERT: A  240 TRP cc_start: 0.9050 (t60) cc_final: 0.8564 (t60)
REVERT: A  642 TYR cc_start: 0.6705 (p90) cc_final: 0.6402 (p90)
REVERT: B   14 PHE cc_start: 0.8813 (t80) cc_final: 0.8597 (t80)
REVERT: B  113 ASP cc_start: 0.7567 (p0) cc_final: 0.7144 (p0)
REVERT: B  522 SER cc_start: 0.9333 (p) cc_final: 0.9126 (p)
REVERT: B  690 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7119 (m-10)
  outliers start: 25
  outliers final: 16
  residues processed: 180
  average time/residue: 0.1785
  time to fit residues: 49.0177
Evaluate side-chains
  158 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
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  190 GLU
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  506 LEU
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  690 PHE
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 47 optimal weight:   50.0000
   chunk 119 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 134 optimal weight:    0.5980
   chunk 40 optimal weight:   30.0000
   chunk 44 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 85 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 628 GLN
B 261 ASN
B 628 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.153491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.108706 restraints weight = 15470.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.105815 restraints weight = 21328.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.107800 restraints weight = 20060.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10892  Z= 0.319
  Angle     :  0.686  10.727  14868  Z= 0.342
  Chirality :  0.044   0.180   1776
  Planarity :  0.005   0.065   1826
  Dihedral  :  5.076  31.807   1484
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 17.13 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.24), residues: 1384
  helix:  1.01 (0.18), residues: 918
  sheet: -2.05 (1.16), residues: 20
  loop : -2.64 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 613 
 HIS   0.004   0.001   HIS A 615 
 PHE   0.029   0.002   PHE A 513 
 TYR   0.040   0.002   TYR B 171 
 ARG   0.003   0.000   ARG A 595 

*********************** 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
  186 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 150
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7807 (mtt-85)
REVERT: A  113 ASP cc_start: 0.7649 (p0) cc_final: 0.7207 (p0)
REVERT: A  226 ARG cc_start: 0.6111 (ptm160) cc_final: 0.5883 (ptm160)
REVERT: A  240 TRP cc_start: 0.9036 (t60) cc_final: 0.8532 (t60)
REVERT: A  519 LEU cc_start: 0.9503 (mm) cc_final: 0.9218 (mp)
REVERT: A  642 TYR cc_start: 0.6761 (p90) cc_final: 0.6423 (p90)
REVERT: B   14 PHE cc_start: 0.8818 (t80) cc_final: 0.8588 (t80)
REVERT: B  423 ILE cc_start: 0.8680 (mm) cc_final: 0.8225 (tp)
  outliers start: 36
  outliers final: 19
  residues processed: 175
  average time/residue: 0.1918
  time to fit residues: 50.5635
Evaluate side-chains
  161 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
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  375 LEU
Chi-restraints excluded: chain A residue  428 MET
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  578 LEU
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 B residue  102 LEU
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  330 CYS
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  599 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 129 optimal weight:    0.8980
   chunk 121 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 105 optimal weight:    0.7980
   chunk 88 optimal weight:    0.4980
   chunk 125 optimal weight:    1.9990
   chunk 132 optimal weight:    0.0970
   chunk 104 optimal weight:    0.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 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 = 0.3835 r_free = 0.3835 target = 0.165059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.120790 restraints weight = 14908.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.120184 restraints weight = 17118.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.121941 restraints weight = 15308.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1948

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= 0.191
  Angle     :  0.660  12.714  14868  Z= 0.318
  Chirality :  0.041   0.166   1776
  Planarity :  0.005   0.064   1826
  Dihedral  :  4.902  31.842   1484
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 18.81 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.24), residues: 1384
  helix:  1.13 (0.18), residues: 916
  sheet: -1.38 (1.27), residues: 20
  loop : -2.57 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 613 
 HIS   0.005   0.001   HIS A 615 
 PHE   0.028   0.001   PHE A 513 
 TYR   0.011   0.001   TYR B 220 
 ARG   0.002   0.000   ARG A 611 

*********************** 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
  193 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 152
  time to evaluate  : 1.096 
Fit side-chains
REVERT: A   29 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7719 (mtt180)
REVERT: A  113 ASP cc_start: 0.7613 (p0) cc_final: 0.7176 (p0)
REVERT: A  226 ARG cc_start: 0.5927 (ptm160) cc_final: 0.5709 (ptm160)
REVERT: A  232 GLU cc_start: 0.6580 (pm20) cc_final: 0.6131 (pm20)
REVERT: A  240 TRP cc_start: 0.8972 (t60) cc_final: 0.8447 (t60)
REVERT: A  519 LEU cc_start: 0.9503 (mm) cc_final: 0.9170 (mp)
REVERT: A  571 CYS cc_start: 0.8405 (m) cc_final: 0.7345 (t)
REVERT: A  642 TYR cc_start: 0.6533 (p90) cc_final: 0.6190 (p90)
REVERT: B   14 PHE cc_start: 0.8877 (t80) cc_final: 0.8651 (t80)
REVERT: B   29 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7610 (mtt180)
REVERT: B  690 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7190 (m-10)
  outliers start: 41
  outliers final: 29
  residues processed: 182
  average time/residue: 0.2001
  time to fit residues: 55.0755
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  : 1.100 
-------------------------------------------------------------------------------
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  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  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 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  198 ASP
Chi-restraints excluded: chain B residue  330 CYS
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  563 MET
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  599 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 137 optimal weight:    0.0570
   chunk 27 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 109 optimal weight:   20.0000
   chunk 48 optimal weight:    0.8980
   chunk 108 optimal weight:   40.0000
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7702

-------------------------------------------------------------------------------
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 = 0.3868 r_free = 0.3868 target = 0.168409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.120231 restraints weight = 14952.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.122102 restraints weight = 11166.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.122975 restraints weight = 9450.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10892  Z= 0.208
  Angle     :  0.652  11.502  14868  Z= 0.314
  Chirality :  0.042   0.161   1776
  Planarity :  0.005   0.071   1826
  Dihedral  :  4.808  31.296   1484
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.67 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.24), residues: 1384
  helix:  1.16 (0.18), residues: 916
  sheet: -1.02 (1.32), residues: 20
  loop : -2.51 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 548 
 HIS   0.005   0.001   HIS A 615 
 PHE   0.026   0.001   PHE A 513 
 TYR   0.011   0.001   TYR B 220 
 ARG   0.003   0.000   ARG A  56 

*********************** 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
  183 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 146
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7779 (mtt-85)
REVERT: A  113 ASP cc_start: 0.7636 (p0) cc_final: 0.7233 (p0)
REVERT: A  240 TRP cc_start: 0.8951 (t60) cc_final: 0.8403 (t60)
REVERT: A  642 TYR cc_start: 0.6618 (p90) cc_final: 0.6289 (p90)
REVERT: B   14 PHE cc_start: 0.8806 (t80) cc_final: 0.8587 (t80)
REVERT: B  520 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8552 (tm-30)
REVERT: B  690 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7220 (m-10)
  outliers start: 37
  outliers final: 29
  residues processed: 173
  average time/residue: 0.1935
  time to fit residues: 50.0194
Evaluate side-chains
  168 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 138
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   99 SER
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  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  563 MET
Chi-restraints excluded: chain A residue  579 ILE
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 B residue  102 LEU
Chi-restraints excluded: chain B residue  146 SER
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  330 CYS
Chi-restraints excluded: chain B residue  462 PHE
Chi-restraints excluded: chain B residue  563 MET
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  599 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 111 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0980
   chunk 126 optimal weight:    0.0770
   chunk 86 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 105 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 134 optimal weight:    0.5980
   chunk 72 optimal weight:    0.3980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.3538

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

Flipped N/Q/H residues before XYZ refinement:
** A 308 GLN ** 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 = 0.3997 r_free = 0.3997 target = 0.179668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.136627 restraints weight = 16004.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.134111 restraints weight = 13062.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.134430 restraints weight = 11976.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10892  Z= 0.165
  Angle     :  0.644  10.676  14868  Z= 0.307
  Chirality :  0.041   0.172   1776
  Planarity :  0.005   0.073   1826
  Dihedral  :  4.659  31.152   1484
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 21.23 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.25), residues: 1384
  helix:  1.26 (0.18), residues: 926
  sheet: -1.04 (1.33), residues: 22
  loop : -2.35 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 548 
 HIS   0.005   0.001   HIS A 615 
 PHE   0.025   0.001   PHE A 513 
 TYR   0.009   0.001   TYR B 517 
 ARG   0.003   0.000   ARG B  56 

*********************** 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
  187 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 154
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7744 (mtt-85)
REVERT: A   63 ARG cc_start: 0.7346 (ttm110) cc_final: 0.7132 (ttm110)
REVERT: A  113 ASP cc_start: 0.7640 (p0) cc_final: 0.7262 (p0)
REVERT: A  183 MET cc_start: 0.8148 (tpp) cc_final: 0.7896 (tpp)
REVERT: A  378 MET cc_start: 0.7397 (mmm) cc_final: 0.6620 (mtp)
REVERT: A  520 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8263 (tm-30)
REVERT: A  571 CYS cc_start: 0.8212 (m) cc_final: 0.7308 (t)
REVERT: A  642 TYR cc_start: 0.6499 (p90) cc_final: 0.6228 (p90)
REVERT: B   14 PHE cc_start: 0.8759 (t80) cc_final: 0.8548 (t80)
REVERT: B  183 MET cc_start: 0.7926 (tpp) cc_final: 0.7721 (tpp)
REVERT: B  378 MET cc_start: 0.7194 (mmm) cc_final: 0.6787 (mmm)
REVERT: B  520 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8609 (tm-30)
REVERT: B  571 CYS cc_start: 0.7866 (m) cc_final: 0.7644 (t)
REVERT: B  690 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7217 (m-10)
  outliers start: 33
  outliers final: 26
  residues processed: 178
  average time/residue: 0.1848
  time to fit residues: 49.0632
Evaluate side-chains
  172 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 SER
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  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  579 ILE
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 B residue  102 LEU
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  462 PHE
Chi-restraints excluded: chain B residue  525 ILE
Chi-restraints excluded: chain B residue  563 MET
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  599 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 58 optimal weight:    2.9990
   chunk 137 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 102 optimal weight:    0.2980
   chunk 71 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 134 optimal weight:    0.5980
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.8980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** 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 = 0.3856 r_free = 0.3856 target = 0.166323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.116923 restraints weight = 16085.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.114716 restraints weight = 12455.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.115523 restraints weight = 11244.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2425

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= 0.202
  Angle     :  0.672  15.239  14868  Z= 0.317
  Chirality :  0.041   0.150   1776
  Planarity :  0.005   0.076   1826
  Dihedral  :  4.607  31.068   1484
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 21.69 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1384
  helix:  1.37 (0.18), residues: 916
  sheet: -0.93 (1.32), residues: 22
  loop : -2.38 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 548 
 HIS   0.002   0.000   HIS A 615 
 PHE   0.025   0.001   PHE A 513 
 TYR   0.019   0.001   TYR A 220 
 ARG   0.002   0.000   ARG A  56 

*********************** 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
  181 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 146
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7725 (mtt-85)
REVERT: A   63 ARG cc_start: 0.7403 (ttm110) cc_final: 0.7160 (ttm110)
REVERT: A  113 ASP cc_start: 0.7741 (p0) cc_final: 0.7354 (p0)
REVERT: A  183 MET cc_start: 0.8177 (tpp) cc_final: 0.7928 (tpp)
REVERT: A  317 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8922 (p)
REVERT: A  378 MET cc_start: 0.7682 (mmm) cc_final: 0.6686 (mtp)
REVERT: A  520 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8384 (tm-30)
REVERT: A  642 TYR cc_start: 0.6436 (p90) cc_final: 0.6158 (p90)
REVERT: B  183 MET cc_start: 0.7972 (tpp) cc_final: 0.7753 (tpp)
REVERT: B  378 MET cc_start: 0.7431 (mmm) cc_final: 0.7047 (mmm)
REVERT: B  520 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8746 (tm-30)
REVERT: B  690 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7175 (m-10)
  outliers start: 35
  outliers final: 27
  residues processed: 171
  average time/residue: 0.1874
  time to fit residues: 48.3235
Evaluate side-chains
  169 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 140
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   99 SER
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  579 ILE
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 B residue  102 LEU
Chi-restraints excluded: chain B residue  146 SER
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  563 MET
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  599 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 126 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 122 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.166281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.116758 restraints weight = 16233.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.115064 restraints weight = 12598.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.115637 restraints weight = 10382.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2478

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= 0.201
  Angle     :  0.672  13.110  14868  Z= 0.316
  Chirality :  0.041   0.144   1776
  Planarity :  0.005   0.078   1826
  Dihedral  :  4.588  31.085   1484
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 22.16 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.25), residues: 1384
  helix:  1.35 (0.18), residues: 914
  sheet: -0.28 (1.39), residues: 20
  loop : -2.40 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 548 
 HIS   0.003   0.000   HIS A 615 
 PHE   0.025   0.001   PHE B  14 
 TYR   0.015   0.001   TYR A 220 
 ARG   0.002   0.000   ARG A  56 

*********************** 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
  183 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 1.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7754 (mtt-85)
REVERT: A   63 ARG cc_start: 0.7391 (ttm110) cc_final: 0.7152 (ttm110)
REVERT: A  113 ASP cc_start: 0.7714 (p0) cc_final: 0.7354 (p0)
REVERT: A  183 MET cc_start: 0.8198 (tpp) cc_final: 0.7932 (tpp)
REVERT: A  520 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: A  642 TYR cc_start: 0.6448 (p90) cc_final: 0.6182 (p90)
REVERT: B  183 MET cc_start: 0.7994 (tpp) cc_final: 0.7778 (tpp)
REVERT: B  378 MET cc_start: 0.7282 (mmm) cc_final: 0.6971 (mmm)
REVERT: B  520 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8720 (tm-30)
REVERT: B  521 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8956 (tt)
REVERT: B  690 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7092 (m-10)
  outliers start: 33
  outliers final: 25
  residues processed: 172
  average time/residue: 0.2176
  time to fit residues: 56.1743
Evaluate side-chains
  172 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   99 SER
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  524 ILE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  579 ILE
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 B residue  102 LEU
Chi-restraints excluded: chain B residue  146 SER
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  521 LEU
Chi-restraints excluded: chain B residue  563 MET
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  599 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 135 optimal weight:    0.0170
   chunk 130 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0170
   chunk 73 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 95 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9980
   chunk 72 optimal weight:    0.1980
   chunk 85 optimal weight:    0.8980
   chunk 106 optimal weight:    3.9990
   chunk 131 optimal weight:    0.6980
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 277 GLN
B 299 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.180201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.136259 restraints weight = 15785.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.135279 restraints weight = 14128.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.135145 restraints weight = 12075.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10892  Z= 0.165
  Angle     :  0.660  14.393  14868  Z= 0.309
  Chirality :  0.041   0.150   1776
  Planarity :  0.005   0.079   1826
  Dihedral  :  4.475  30.565   1484
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 22.53 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.25), residues: 1384
  helix:  1.42 (0.18), residues: 918
  sheet: -0.61 (1.34), residues: 22
  loop : -2.29 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 548 
 HIS   0.002   0.000   HIS A 615 
 PHE   0.017   0.001   PHE B 640 
 TYR   0.014   0.001   TYR A 220 
 ARG   0.002   0.000   ARG A 661 

********************** 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
  173 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 1.260 
Fit side-chains
REVERT: A   29 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7709 (mtt180)
REVERT: A   63 ARG cc_start: 0.7352 (ttm110) cc_final: 0.7099 (ttm110)
REVERT: A  113 ASP cc_start: 0.7550 (p0) cc_final: 0.7206 (p0)
REVERT: A  183 MET cc_start: 0.8129 (tpp) cc_final: 0.7890 (tpp)
REVERT: A  520 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8385 (tm-30)
REVERT: A  571 CYS cc_start: 0.8220 (m) cc_final: 0.7481 (t)
REVERT: A  642 TYR cc_start: 0.6560 (p90) cc_final: 0.6296 (p90)
REVERT: B  183 MET cc_start: 0.7879 (tpp) cc_final: 0.7669 (tpp)
REVERT: B  378 MET cc_start: 0.7294 (mmm) cc_final: 0.6922 (mmm)
REVERT: B  520 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8660 (tm-30)
REVERT: B  690 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7303 (m-10)
  outliers start: 28
  outliers final: 19
  residues processed: 164
  average time/residue: 0.1984
  time to fit residues: 48.6943
Evaluate side-chains
  162 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   99 SER
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  524 ILE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain B residue  102 LEU
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  599 LEU
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 93 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0570
   chunk 19 optimal weight:    0.0070
   chunk 81 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 40 optimal weight:   20.0000
   chunk 33 optimal weight:    0.6980
   chunk 74 optimal weight:    0.2980
   chunk 78 optimal weight:    2.9990
   chunk 121 optimal weight:    0.7980
   overall best weight:    0.3316

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

Flipped N/Q/H residues before XYZ refinement:
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3863 r_free = 0.3863 target = 0.167169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.117108 restraints weight = 16247.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.115146 restraints weight = 13503.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.115762 restraints weight = 11654.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2811

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= 0.168
  Angle     :  0.672  14.635  14868  Z= 0.313
  Chirality :  0.040   0.149   1776
  Planarity :  0.005   0.079   1826
  Dihedral  :  4.449  32.503   1484
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 22.91 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1384
  helix:  1.44 (0.18), residues: 918
  sheet: -0.55 (1.33), residues: 22
  loop : -2.29 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 548 
 HIS   0.002   0.000   HIS A 615 
 PHE   0.020   0.001   PHE A 690 
 TYR   0.016   0.001   TYR A 377 
 ARG   0.002   0.000   ARG A  56 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2944.71 seconds
wall clock time: 53 minutes 49.48 seconds (3229.48 seconds total)