Starting phenix.real_space_refine
on Wed Sep 17 09:05:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cp5_45800/09_2025/9cp5_45800.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cp5_45800/09_2025/9cp5_45800.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cp5_45800/09_2025/9cp5_45800.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cp5_45800/09_2025/9cp5_45800.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cp5_45800/09_2025/9cp5_45800.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cp5_45800/09_2025/9cp5_45800.cif"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 sd=   0.085
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     Cl      1      4.86       5
     C    4842      2.51       5
     N    1182      2.21       5
     O    1367      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7450
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 538, 4253
          Classifications: {'peptide': 538}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 25, 'TRANS': 512}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "H"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1599
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "L"
      Number of atoms: 1597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1597
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.82, per 1000 atoms: 0.24
  Number of scatterers: 7450
  At special positions: 0
  Unit cell: (78.934, 85.404, 151.398, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      58     16.00
     O    1367      8.00
     N    1182      7.00
     C    4842      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 171 " - pdb=" SG  CYS A 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 146 " - pdb=" SG  CYS H 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.55
  Conformation dependent library (CDL) restraints added in 358.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1780

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 9 sheets defined
      45.2% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 68
      removed outlier: 3.835A  pdb=" N   GLU A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE A  68 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 74
    Processing helix  chain 'A' and resid 74 through 83
      removed outlier: 3.697A  pdb=" N   TYR A  78 " --> pdb=" O   TRP A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 99
    Processing helix  chain 'A' and resid 99 through 115
      removed outlier: 3.700A  pdb=" N   VAL A 103 " --> pdb=" O   CYS A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 126
    Processing helix  chain 'A' and resid 130 through 147
      removed outlier: 3.908A  pdb=" N   TYR A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 162
      removed outlier: 4.222A  pdb=" N   PHE A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 170
      removed outlier: 3.686A  pdb=" N   ALA A 169 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   THR A 170 " --> pdb=" O   PRO A 167 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 166 through 170'
    Processing helix  chain 'A' and resid 201 through 211
      removed outlier: 3.604A  pdb=" N   GLU A 208 " --> pdb=" O   MET A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 245
    Processing helix  chain 'A' and resid 259 through 275
      removed outlier: 3.643A  pdb=" N   THR A 274 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 287
      removed outlier: 3.732A  pdb=" N   GLY A 281 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 4.384A  pdb=" N   TRP A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 324
      removed outlier: 4.152A  pdb=" N   ALA A 319 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ASN A 324 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 363
      removed outlier: 3.836A  pdb=" N   ASP A 333 " --> pdb=" O   ASN A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 370
      removed outlier: 3.659A  pdb=" N   GLU A 369 " --> pdb=" O   PRO A 366 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL A 370 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 366 through 370'
    Processing helix  chain 'A' and resid 376 through 379
    Processing helix  chain 'A' and resid 380 through 386
    Processing helix  chain 'A' and resid 391 through 426
      removed outlier: 3.680A  pdb=" N   TRP A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 431
      removed outlier: 3.971A  pdb=" N   PHE A 430 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ARG A 431 " --> pdb=" O   PRO A 427 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 426 through 431'
    Processing helix  chain 'A' and resid 435 through 452
    Processing helix  chain 'A' and resid 453 through 455
      No H-bonds generated for 'chain 'A' and resid 453 through 455'
    Processing helix  chain 'A' and resid 458 through 470
      removed outlier: 4.129A  pdb=" N   ILE A 462 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 490
    Processing helix  chain 'A' and resid 492 through 505
    Processing helix  chain 'A' and resid 510 through 518
    Processing helix  chain 'A' and resid 519 through 534
    Processing helix  chain 'A' and resid 547 through 563
    Processing helix  chain 'A' and resid 563 through 576
    Processing helix  chain 'A' and resid 579 through 589
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.638A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.672A  pdb=" N   ASP L  83 " --> pdb=" O   GLU L  80 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ALA L  84 " --> pdb=" O   ALA L  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 80 through 84'
    Processing helix  chain 'L' and resid 122 through 128
      removed outlier: 3.651A  pdb=" N   LEU L 126 " --> pdb=" O   SER L 123 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   SER L 128 " --> pdb=" O   GLN L 125 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 189
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.576A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER H  21 " --> pdb=" O   SER H   7 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU H  18 " --> pdb=" O   MET H  83 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   HIS H  80 " --> pdb=" O   SER H  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.240A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 126 through 130
      removed outlier: 3.589A  pdb=" N   SER H 126 " --> pdb=" O   LYS H 149 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   GLY H 145 " --> pdb=" O   LEU H 130 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   TYR H 181 " --> pdb=" O   GLY H 150 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 130
      removed outlier: 3.589A  pdb=" N   SER H 126 " --> pdb=" O   LYS H 149 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   GLY H 145 " --> pdb=" O   LEU H 130 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   TYR H 181 " --> pdb=" O   GLY H 150 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   THR H 182 " --> pdb=" O   VAL H 175 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL H 175 " --> pdb=" O   THR H 182 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160
      removed outlier: 3.738A  pdb=" N   THR H 159 " --> pdb=" O   ASN H 202 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASN H 202 " --> pdb=" O   THR H 159 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 5
      removed outlier: 3.790A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  76 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TYR L  72 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   SER L  71 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.818A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 117 through 119
      removed outlier: 6.302A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 154 through 156
      removed outlier: 3.851A  pdb=" N   TRP L 149 " --> pdb=" O   ARG L 156 " (cutoff:3.500A)

    386 hydrogen bonds defined for protein.
    1110 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2252
        1.34 -     1.46: 2025
        1.46 -     1.58: 3300
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 7659
  Sorted by residual:
  bond pdb=" C   PRO A 508 "
       pdb=" N   PRO A 509 "
    ideal  model  delta    sigma   weight residual
    1.334  1.344 -0.011 8.40e-03 1.42e+04 1.66e+00
  bond pdb=" N   ASN L 213 "
       pdb=" CA  ASN L 213 "
    ideal  model  delta    sigma   weight residual
    1.458  1.482 -0.024 1.90e-02 2.77e+03 1.61e+00
  bond pdb=" C   ILE A 565 "
       pdb=" N   PRO A 566 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.015 1.23e-02 6.61e+03 1.43e+00
  bond pdb=" CA  ILE A 543 "
       pdb=" CB  ILE A 543 "
    ideal  model  delta    sigma   weight residual
    1.540  1.556 -0.016 1.36e-02 5.41e+03 1.40e+00
  bond pdb=" C   SER A 392 "
       pdb=" N   PRO A 393 "
    ideal  model  delta    sigma   weight residual
    1.335  1.349 -0.014 1.28e-02 6.10e+03 1.28e+00
  ... (remaining 7654 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 10073
        1.68 -     3.36: 306
        3.36 -     5.04: 37
        5.04 -     6.73: 14
        6.73 -     8.41: 14
  Bond angle restraints: 10444
  Sorted by residual:
  angle pdb=" C   SER L  51 "
        pdb=" N   THR L  52 "
        pdb=" CA  THR L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  129.56   -8.02 1.91e+00 2.74e-01 1.77e+01
  angle pdb=" C   TYR A 191 "
        pdb=" N   SER A 192 "
        pdb=" CA  SER A 192 "
      ideal   model   delta    sigma   weight residual
     121.54  129.29   -7.75 1.91e+00 2.74e-01 1.65e+01
  angle pdb=" C   ARG L 212 "
        pdb=" N   ASN L 213 "
        pdb=" CA  ASN L 213 "
      ideal   model   delta    sigma   weight residual
     121.70  128.44   -6.74 1.80e+00 3.09e-01 1.40e+01
  angle pdb=" C   PRO A 509 "
        pdb=" N   SER A 510 "
        pdb=" CA  SER A 510 "
      ideal   model   delta    sigma   weight residual
     121.54  128.33   -6.79 1.91e+00 2.74e-01 1.27e+01
  angle pdb=" C   GLY A 578 "
        pdb=" N   THR A 579 "
        pdb=" CA  THR A 579 "
      ideal   model   delta    sigma   weight residual
     121.54  128.22   -6.68 1.91e+00 2.74e-01 1.22e+01
  ... (remaining 10439 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4016
       17.95 -    35.90: 331
       35.90 -    53.85: 68
       53.85 -    71.80: 8
       71.80 -    89.75: 11
  Dihedral angle restraints: 4434
    sinusoidal: 1641
      harmonic: 2793
  Sorted by residual:
  dihedral pdb=" CB  CYS A 171 "
           pdb=" SG  CYS A 171 "
           pdb=" SG  CYS A 180 "
           pdb=" CB  CYS A 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.42   76.42     1      1.00e+01 1.00e-02 7.35e+01
  dihedral pdb=" CA  MET A 517 "
           pdb=" C   MET A 517 "
           pdb=" N   ILE A 518 "
           pdb=" CA  ILE A 518 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.49  -18.51     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  THR A 579 "
           pdb=" C   THR A 579 "
           pdb=" N   LEU A 580 "
           pdb=" CA  LEU A 580 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.65  -16.35     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4431 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 825
       0.044 -    0.088: 258
       0.088 -    0.132: 79
       0.132 -    0.176: 12
       0.176 -    0.220: 4
  Chirality restraints: 1178
  Sorted by residual:
  chirality pdb=" CB  ILE A 543 "
            pdb=" CA  ILE A 543 "
            pdb=" CG1 ILE A 543 "
            pdb=" CG2 ILE A 543 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CG  LEU A 455 "
            pdb=" CB  LEU A 455 "
            pdb=" CD1 LEU A 455 "
            pdb=" CD2 LEU A 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.79e-01
  chirality pdb=" CA  TYR A 382 "
            pdb=" N   TYR A 382 "
            pdb=" C   TYR A 382 "
            pdb=" CB  TYR A 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.43e-01
  ... (remaining 1175 not shown)

  Planarity restraints: 1292
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 350 "   -0.014 2.00e-02 2.50e+03   1.55e-02 4.19e+00
        pdb=" CG  PHE A 350 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 350 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 350 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 350 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 350 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 350 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 207 "    0.009 2.00e-02 2.50e+03   1.88e-02 3.53e+00
        pdb=" C   TRP A 207 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   TRP A 207 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 208 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 365 "   -0.028 5.00e-02 4.00e+02   4.20e-02 2.83e+00
        pdb=" N   PRO A 366 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 366 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 366 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1289 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1371
        2.77 -     3.30: 6884
        3.30 -     3.84: 12734
        3.84 -     4.37: 14081
        4.37 -     4.90: 25096
  Nonbonded interactions: 60166
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU L 106 "
            pdb=" OH  TYR L 174 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   CYS A  98 "
            pdb=" OG1 THR A 520 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   SER H 140 "
            pdb=" OG  SER H 191 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" ND2 ASN A  83 "
            pdb=" OD2 ASP A 301 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" OG  SER L  64 "
            pdb=" OG1 THR L  75 "
     model   vdw
     2.318 3.040
  ... (remaining 60161 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.460
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7664  Z= 0.166
  Angle     :  0.734   8.408  10454  Z= 0.381
  Chirality :  0.048   0.220   1178
  Planarity :  0.005   0.042   1292
  Dihedral  : 14.363  89.746   2639
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.25), residues: 958
  helix: -0.55 (0.24), residues: 380
  sheet: -1.17 (0.39), residues: 182
  loop : -1.62 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  44 
 TYR   0.020   0.001   TYR A 382 
 PHE   0.036   0.002   PHE A 350 
 TRP   0.016   0.001   TRP A 549 
 HIS   0.003   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 7659)
  covalent geometry    : angle       0.73350 (10444)
  SS BOND              : bond        0.00205 (    5)
  SS BOND              : angle       1.16908 (   10)
  hydrogen bonds       : bond        0.19299 (  375)
  hydrogen bonds       : angle       8.06078 ( 1110)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7308 (mm-30)
REVERT: A   97 ILE cc_start: 0.8067 (mm) cc_final: 0.7659 (pt)
REVERT: A  184 GLN cc_start: 0.7409 (mm110) cc_final: 0.7094 (mm-40)
REVERT: A  220 HIS cc_start: 0.7678 (m-70) cc_final: 0.7340 (m-70)
REVERT: A  226 TRP cc_start: 0.6837 (m100) cc_final: 0.6196 (p-90)
REVERT: A  230 LEU cc_start: 0.8077 (mm) cc_final: 0.7839 (tp)
REVERT: A  299 TRP cc_start: 0.8308 (m100) cc_final: 0.7745 (m100)
REVERT: A  335 ILE cc_start: 0.7893 (mm) cc_final: 0.7473 (tp)
REVERT: A  336 MET cc_start: 0.7985 (ptt) cc_final: 0.7733 (ptp)
REVERT: A  339 CYS cc_start: 0.7004 (t) cc_final: 0.6361 (m)
REVERT: A  389 MET cc_start: 0.7499 (mmm) cc_final: 0.6993 (mtt)
REVERT: A  416 GLU cc_start: 0.8490 (tt0) cc_final: 0.8064 (tp30)
REVERT: A  444 SER cc_start: 0.8679 (m) cc_final: 0.8461 (p)
REVERT: A  457 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6943 (tt0)
REVERT: A  518 ILE cc_start: 0.8436 (pt) cc_final: 0.8200 (tp)
REVERT: A  551 TYR cc_start: 0.7117 (m-10) cc_final: 0.6889 (m-10)
REVERT: A  557 MET cc_start: 0.7669 (ppp) cc_final: 0.6739 (ppp)
REVERT: H    7 SER cc_start: 0.7673 (t) cc_final: 0.7446 (p)
REVERT: H   13 LYS cc_start: 0.8789 (mptt) cc_final: 0.8504 (mptt)
REVERT: H  116 THR cc_start: 0.8533 (m) cc_final: 0.8322 (p)
REVERT: L   13 THR cc_start: 0.8634 (p) cc_final: 0.8252 (p)
REVERT: L   50 TYR cc_start: 0.9116 (p90) cc_final: 0.8725 (p90)
REVERT: L  107 MET cc_start: 0.7964 (mmm) cc_final: 0.7459 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.1015
  time to fit residues: 30.1098
Evaluate side-chains
  145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN
A 160 ASN
** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  39 GLN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 167 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.177226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.144632 restraints weight = 10752.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.147979 restraints weight = 6638.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.150246 restraints weight = 4838.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.151654 restraints weight = 3923.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.152253 restraints weight = 3422.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7664  Z= 0.150
  Angle     :  0.626   5.833  10454  Z= 0.326
  Chirality :  0.043   0.195   1178
  Planarity :  0.004   0.039   1292
  Dihedral  :  4.236  18.147   1039
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 12.75 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.27), residues: 958
  helix:  0.33 (0.26), residues: 388
  sheet: -0.83 (0.40), residues: 172
  loop : -1.51 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 123 
 TYR   0.017   0.002   TYR H 151 
 PHE   0.018   0.002   PHE A 350 
 TRP   0.032   0.001   TRP A 244 
 HIS   0.007   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7659)
  covalent geometry    : angle       0.62547 (10444)
  SS BOND              : bond        0.00263 (    5)
  SS BOND              : angle       0.81867 (   10)
  hydrogen bonds       : bond        0.04863 (  375)
  hydrogen bonds       : angle       5.80859 ( 1110)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 ILE cc_start: 0.8431 (mm) cc_final: 0.8203 (mt)
REVERT: A  226 TRP cc_start: 0.6799 (m100) cc_final: 0.6577 (p-90)
REVERT: A  299 TRP cc_start: 0.7882 (m100) cc_final: 0.7670 (m100)
REVERT: A  335 ILE cc_start: 0.7821 (mm) cc_final: 0.7586 (tp)
REVERT: A  557 MET cc_start: 0.7345 (ppp) cc_final: 0.6845 (ppp)
REVERT: H   13 LYS cc_start: 0.8712 (mptt) cc_final: 0.8484 (tppt)
REVERT: H   32 TYR cc_start: 0.7349 (m-10) cc_final: 0.7092 (m-10)
REVERT: H  151 TYR cc_start: 0.7892 (p90) cc_final: 0.7685 (p90)
REVERT: L    1 GLU cc_start: 0.7563 (tp30) cc_final: 0.6912 (tp30)
REVERT: L  150 LYS cc_start: 0.5421 (mtpt) cc_final: 0.5047 (mttt)
REVERT: L  176 MET cc_start: 0.5850 (tpt) cc_final: 0.5499 (tpt)
  outliers start: 11
  outliers final: 8
  residues processed: 161
  average time/residue: 0.0946
  time to fit residues: 20.4915
Evaluate side-chains
  137 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 37 optimal weight:    0.2980
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0470
   chunk 25 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 34 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 ASN
H 103 GLN
L   2 ASN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.177608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.144599 restraints weight = 10732.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.147999 restraints weight = 6675.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.150239 restraints weight = 4890.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.151721 restraints weight = 3993.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.152486 restraints weight = 3497.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7664  Z= 0.127
  Angle     :  0.591   6.000  10454  Z= 0.303
  Chirality :  0.043   0.209   1178
  Planarity :  0.004   0.047   1292
  Dihedral  :  4.158  17.925   1039
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 15.97 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.27), residues: 958
  helix:  0.59 (0.26), residues: 390
  sheet: -0.67 (0.40), residues: 170
  loop : -1.39 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  56 
 TYR   0.015   0.001   TYR A 146 
 PHE   0.015   0.001   PHE A 358 
 TRP   0.020   0.001   TRP L 164 
 HIS   0.004   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7659)
  covalent geometry    : angle       0.59039 (10444)
  SS BOND              : bond        0.00221 (    5)
  SS BOND              : angle       0.75438 (   10)
  hydrogen bonds       : bond        0.04311 (  375)
  hydrogen bonds       : angle       5.45731 ( 1110)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 ILE cc_start: 0.8564 (mm) cc_final: 0.8307 (mt)
REVERT: A  220 HIS cc_start: 0.6717 (m-70) cc_final: 0.6476 (m170)
REVERT: A  226 TRP cc_start: 0.6813 (m100) cc_final: 0.6532 (p-90)
REVERT: A  244 TRP cc_start: 0.7012 (t60) cc_final: 0.6722 (t60)
REVERT: A  299 TRP cc_start: 0.7820 (m100) cc_final: 0.7602 (m100)
REVERT: A  557 MET cc_start: 0.7295 (ppp) cc_final: 0.6954 (ppp)
REVERT: H   32 TYR cc_start: 0.7462 (m-10) cc_final: 0.7178 (m-10)
REVERT: H  151 TYR cc_start: 0.7955 (p90) cc_final: 0.7741 (p90)
REVERT: L    1 GLU cc_start: 0.7460 (tp30) cc_final: 0.6879 (tp30)
REVERT: L    2 ASN cc_start: 0.7806 (m110) cc_final: 0.7118 (m-40)
REVERT: L  150 LYS cc_start: 0.5343 (mtpt) cc_final: 0.5030 (mttt)
  outliers start: 9
  outliers final: 5
  residues processed: 139
  average time/residue: 0.0970
  time to fit residues: 18.0991
Evaluate side-chains
  129 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 124
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 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 = 0.4321 r_free = 0.4321 target = 0.183392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.144495 restraints weight = 11950.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.148780 restraints weight = 6438.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.151544 restraints weight = 4474.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.153298 restraints weight = 3585.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.154075 restraints weight = 3123.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7664  Z= 0.176
  Angle     :  0.614   6.613  10454  Z= 0.315
  Chirality :  0.044   0.175   1178
  Planarity :  0.004   0.037   1292
  Dihedral  :  4.227  17.963   1039
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.20 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.28), residues: 958
  helix:  0.62 (0.26), residues: 392
  sheet: -0.50 (0.39), residues: 187
  loop : -1.25 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 332 
 TYR   0.015   0.002   TYR A 146 
 PHE   0.014   0.002   PHE A 496 
 TRP   0.029   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 7659)
  covalent geometry    : angle       0.61360 (10444)
  SS BOND              : bond        0.00302 (    5)
  SS BOND              : angle       0.88149 (   10)
  hydrogen bonds       : bond        0.04223 (  375)
  hydrogen bonds       : angle       5.28627 ( 1110)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.6312 (t80)
REVERT: A   97 ILE cc_start: 0.8523 (mm) cc_final: 0.8197 (mt)
REVERT: A  226 TRP cc_start: 0.7169 (m100) cc_final: 0.6559 (p-90)
REVERT: A  244 TRP cc_start: 0.7699 (t60) cc_final: 0.7350 (t60)
REVERT: A  299 TRP cc_start: 0.8233 (m100) cc_final: 0.7825 (m100)
REVERT: A  557 MET cc_start: 0.7452 (ppp) cc_final: 0.7225 (ppp)
REVERT: H   32 TYR cc_start: 0.7849 (m-10) cc_final: 0.7554 (m-10)
REVERT: H  151 TYR cc_start: 0.8068 (p90) cc_final: 0.7550 (p90)
REVERT: L    2 ASN cc_start: 0.8187 (m110) cc_final: 0.7634 (m-40)
REVERT: L   53 SER cc_start: 0.8392 (m) cc_final: 0.8191 (p)
REVERT: L  150 LYS cc_start: 0.5659 (mtpt) cc_final: 0.5378 (mttt)
  outliers start: 15
  outliers final: 10
  residues processed: 138
  average time/residue: 0.0990
  time to fit residues: 18.3253
Evaluate side-chains
  132 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 324 ASN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.183521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.145024 restraints weight = 11697.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.149325 restraints weight = 6377.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.152099 restraints weight = 4429.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.153840 restraints weight = 3551.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.154574 restraints weight = 3092.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7664  Z= 0.153
  Angle     :  0.600   6.260  10454  Z= 0.306
  Chirality :  0.043   0.147   1178
  Planarity :  0.004   0.057   1292
  Dihedral  :  4.194  17.225   1039
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.56 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.28), residues: 958
  helix:  0.81 (0.26), residues: 385
  sheet: -0.55 (0.38), residues: 190
  loop : -1.10 (0.33), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 292 
 TYR   0.014   0.001   TYR A 146 
 PHE   0.011   0.001   PHE A 358 
 TRP   0.031   0.001   TRP L 164 
 HIS   0.004   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7659)
  covalent geometry    : angle       0.59986 (10444)
  SS BOND              : bond        0.00223 (    5)
  SS BOND              : angle       0.72924 (   10)
  hydrogen bonds       : bond        0.04029 (  375)
  hydrogen bonds       : angle       5.13614 ( 1110)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.6500 (t80)
REVERT: A   97 ILE cc_start: 0.8517 (mm) cc_final: 0.8178 (mt)
REVERT: A  147 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7704 (t80)
REVERT: A  226 TRP cc_start: 0.7046 (m100) cc_final: 0.6539 (p-90)
REVERT: A  299 TRP cc_start: 0.8221 (m100) cc_final: 0.7756 (m100)
REVERT: A  339 CYS cc_start: 0.7781 (t) cc_final: 0.6849 (m)
REVERT: H   32 TYR cc_start: 0.7970 (m-10) cc_final: 0.7753 (m-10)
REVERT: L   53 SER cc_start: 0.8343 (m) cc_final: 0.8094 (p)
REVERT: L  107 MET cc_start: 0.7836 (mmm) cc_final: 0.7465 (mmt)
REVERT: L  150 LYS cc_start: 0.5649 (mtpt) cc_final: 0.5329 (mttt)
REVERT: L  164 TRP cc_start: 0.7786 (m-90) cc_final: 0.7563 (m-90)
  outliers start: 18
  outliers final: 11
  residues processed: 138
  average time/residue: 0.0905
  time to fit residues: 16.7756
Evaluate side-chains
  128 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  147 TYR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  206 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 48 optimal weight:    0.3980
   chunk 54 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0980
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 9 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0040
   overall best weight:    0.2392

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

Flipped N/Q/H residues before XYZ refinement:
A 464 GLN
A 541 ASN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.188273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.150866 restraints weight = 11602.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.155301 restraints weight = 6210.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.158124 restraints weight = 4273.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.159614 restraints weight = 3409.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.160859 restraints weight = 2996.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.4089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7664  Z= 0.111
  Angle     :  0.584   7.939  10454  Z= 0.294
  Chirality :  0.041   0.149   1178
  Planarity :  0.004   0.043   1292
  Dihedral  :  3.989  16.430   1039
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.81 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.28), residues: 958
  helix:  1.01 (0.27), residues: 386
  sheet: -0.50 (0.38), residues: 190
  loop : -1.10 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 292 
 TYR   0.012   0.001   TYR H 151 
 PHE   0.015   0.001   PHE A 358 
 TRP   0.021   0.001   TRP L 164 
 HIS   0.004   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7659)
  covalent geometry    : angle       0.58341 (10444)
  SS BOND              : bond        0.00209 (    5)
  SS BOND              : angle       0.72185 (   10)
  hydrogen bonds       : bond        0.03714 (  375)
  hydrogen bonds       : angle       4.93331 ( 1110)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.6598 (t80)
REVERT: A   97 ILE cc_start: 0.8530 (mm) cc_final: 0.8200 (mt)
REVERT: A  121 CYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8378 (p)
REVERT: A  147 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7871 (t80)
REVERT: A  226 TRP cc_start: 0.7008 (m100) cc_final: 0.6468 (p-90)
REVERT: A  244 TRP cc_start: 0.7629 (t60) cc_final: 0.7298 (t60)
REVERT: A  299 TRP cc_start: 0.8123 (m100) cc_final: 0.7561 (m100)
REVERT: A  339 CYS cc_start: 0.7576 (t) cc_final: 0.6889 (m)
REVERT: A  464 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8463 (tp-100)
REVERT: A  517 MET cc_start: 0.7496 (mmm) cc_final: 0.7145 (mmm)
REVERT: H   82 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7646 (mm-30)
REVERT: H   94 TYR cc_start: 0.8546 (m-80) cc_final: 0.8256 (m-80)
REVERT: H  101 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8825 (t)
REVERT: H  151 TYR cc_start: 0.8205 (p90) cc_final: 0.7766 (p90)
REVERT: L  107 MET cc_start: 0.7854 (mmm) cc_final: 0.7496 (mmt)
REVERT: L  164 TRP cc_start: 0.7681 (m-90) cc_final: 0.7332 (m100)
  outliers start: 22
  outliers final: 12
  residues processed: 144
  average time/residue: 0.0858
  time to fit residues: 16.8688
Evaluate side-chains
  138 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  147 TYR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  101 VAL
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 THR
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  207 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0050
   chunk 91 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 46 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 464 GLN
L   2 ASN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.186308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.149035 restraints weight = 11711.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.153254 restraints weight = 6268.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.156039 restraints weight = 4327.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.157754 restraints weight = 3445.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.158823 restraints weight = 2995.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.3646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7664  Z= 0.125
  Angle     :  0.596   8.706  10454  Z= 0.300
  Chirality :  0.042   0.146   1178
  Planarity :  0.004   0.040   1292
  Dihedral  :  3.987  15.564   1039
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.93 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.28), residues: 958
  helix:  1.10 (0.27), residues: 387
  sheet: -0.44 (0.39), residues: 184
  loop : -1.07 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 292 
 TYR   0.014   0.001   TYR A 310 
 PHE   0.022   0.001   PHE A 531 
 TRP   0.016   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7659)
  covalent geometry    : angle       0.59548 (10444)
  SS BOND              : bond        0.00231 (    5)
  SS BOND              : angle       0.75784 (   10)
  hydrogen bonds       : bond        0.03696 (  375)
  hydrogen bonds       : angle       4.86983 ( 1110)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.6522 (t80)
REVERT: A   97 ILE cc_start: 0.8441 (mm) cc_final: 0.8136 (mt)
REVERT: A  147 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7933 (t80)
REVERT: A  226 TRP cc_start: 0.6992 (m100) cc_final: 0.6497 (p-90)
REVERT: A  244 TRP cc_start: 0.7699 (t60) cc_final: 0.7479 (t60)
REVERT: A  299 TRP cc_start: 0.8189 (m100) cc_final: 0.7606 (m100)
REVERT: A  426 TYR cc_start: 0.7482 (m-10) cc_final: 0.7207 (m-80)
REVERT: A  443 LEU cc_start: 0.8674 (tp) cc_final: 0.8438 (tp)
REVERT: A  464 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8244 (tp40)
REVERT: A  503 MET cc_start: 0.8453 (ttm) cc_final: 0.8211 (ttt)
REVERT: H   94 TYR cc_start: 0.8660 (m-80) cc_final: 0.8258 (m-80)
REVERT: H  151 TYR cc_start: 0.8213 (p90) cc_final: 0.7806 (p90)
REVERT: L   50 TYR cc_start: 0.9023 (p90) cc_final: 0.8773 (p90)
REVERT: L  164 TRP cc_start: 0.7730 (m-90) cc_final: 0.7281 (m100)
  outliers start: 19
  outliers final: 13
  residues processed: 137
  average time/residue: 0.0885
  time to fit residues: 16.5125
Evaluate side-chains
  133 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  147 TYR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  156 VAL
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 THR
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  207 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0970
   chunk 90 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 464 GLN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.186024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.148271 restraints weight = 11834.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.152616 restraints weight = 6293.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.155382 restraints weight = 4335.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.157126 restraints weight = 3460.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.157872 restraints weight = 3006.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7664  Z= 0.130
  Angle     :  0.603   7.142  10454  Z= 0.303
  Chirality :  0.042   0.141   1178
  Planarity :  0.004   0.038   1292
  Dihedral  :  3.992  15.660   1039
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.30 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.28), residues: 958
  helix:  1.14 (0.27), residues: 387
  sheet: -0.45 (0.39), residues: 184
  loop : -1.02 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  44 
 TYR   0.015   0.001   TYR A 551 
 PHE   0.016   0.001   PHE A 531 
 TRP   0.015   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7659)
  covalent geometry    : angle       0.60308 (10444)
  SS BOND              : bond        0.00237 (    5)
  SS BOND              : angle       0.74237 (   10)
  hydrogen bonds       : bond        0.03769 (  375)
  hydrogen bonds       : angle       4.84693 ( 1110)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6661 (t80)
REVERT: A   97 ILE cc_start: 0.8475 (mm) cc_final: 0.8178 (mt)
REVERT: A  121 CYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8421 (p)
REVERT: A  147 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7798 (t80)
REVERT: A  226 TRP cc_start: 0.6988 (m100) cc_final: 0.6601 (p-90)
REVERT: A  244 TRP cc_start: 0.7740 (t60) cc_final: 0.7517 (t60)
REVERT: A  299 TRP cc_start: 0.8093 (m100) cc_final: 0.7607 (m100)
REVERT: A  339 CYS cc_start: 0.7526 (t) cc_final: 0.6933 (m)
REVERT: A  426 TYR cc_start: 0.7409 (m-10) cc_final: 0.7137 (m-80)
REVERT: A  464 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8305 (tp40)
REVERT: A  517 MET cc_start: 0.7629 (mmm) cc_final: 0.7347 (mmm)
REVERT: H   94 TYR cc_start: 0.8710 (m-80) cc_final: 0.8319 (m-80)
REVERT: L   11 MET cc_start: 0.6453 (mmt) cc_final: 0.5863 (mmt)
REVERT: L  164 TRP cc_start: 0.7690 (m-90) cc_final: 0.7357 (m-90)
  outliers start: 19
  outliers final: 14
  residues processed: 140
  average time/residue: 0.0942
  time to fit residues: 17.7456
Evaluate side-chains
  141 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  147 TYR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  156 VAL
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 THR
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  207 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 80 optimal weight:    0.1980
   chunk 56 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0040
   chunk 76 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 73 optimal weight:    5.9990
   overall best weight:    1.0396

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 162 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 = 0.4315 r_free = 0.4315 target = 0.182690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.144672 restraints weight = 11603.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.148963 restraints weight = 6303.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.151669 restraints weight = 4384.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.153201 restraints weight = 3522.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.154314 restraints weight = 3092.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7664  Z= 0.180
  Angle     :  0.643   7.262  10454  Z= 0.326
  Chirality :  0.044   0.143   1178
  Planarity :  0.004   0.038   1292
  Dihedral  :  4.114  15.913   1039
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 20.67 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.28), residues: 958
  helix:  1.09 (0.27), residues: 387
  sheet: -0.64 (0.38), residues: 190
  loop : -0.98 (0.34), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  87 
 TYR   0.037   0.002   TYR H 151 
 PHE   0.018   0.002   PHE A 466 
 TRP   0.014   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 7659)
  covalent geometry    : angle       0.64260 (10444)
  SS BOND              : bond        0.00358 (    5)
  SS BOND              : angle       1.04521 (   10)
  hydrogen bonds       : bond        0.03945 (  375)
  hydrogen bonds       : angle       4.96477 ( 1110)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.6435 (t80)
REVERT: A   97 ILE cc_start: 0.8474 (mm) cc_final: 0.8182 (mt)
REVERT: A  121 CYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7737 (p)
REVERT: A  147 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7699 (t80)
REVERT: A  226 TRP cc_start: 0.7096 (m100) cc_final: 0.6709 (p-90)
REVERT: A  244 TRP cc_start: 0.7871 (t60) cc_final: 0.7627 (t60)
REVERT: A  299 TRP cc_start: 0.8189 (m100) cc_final: 0.7750 (m100)
REVERT: A  339 CYS cc_start: 0.7637 (t) cc_final: 0.6789 (m)
REVERT: A  517 MET cc_start: 0.7666 (mmm) cc_final: 0.7362 (mmm)
REVERT: L   11 MET cc_start: 0.6576 (mmt) cc_final: 0.5969 (mmt)
REVERT: L   53 SER cc_start: 0.8281 (m) cc_final: 0.8064 (p)
REVERT: L  164 TRP cc_start: 0.7764 (m-90) cc_final: 0.7487 (m-90)
  outliers start: 17
  outliers final: 13
  residues processed: 137
  average time/residue: 0.0910
  time to fit residues: 16.8704
Evaluate side-chains
  136 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  147 TYR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 THR
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  207 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 71 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 464 GLN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.183666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.145756 restraints weight = 11695.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.150094 restraints weight = 6307.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.152801 restraints weight = 4370.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.154508 restraints weight = 3504.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.155358 restraints weight = 3045.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.4029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7664  Z= 0.158
  Angle     :  0.648   7.641  10454  Z= 0.328
  Chirality :  0.043   0.137   1178
  Planarity :  0.004   0.037   1292
  Dihedral  :  4.121  15.876   1039
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 21.53 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.28), residues: 958
  helix:  1.08 (0.27), residues: 387
  sheet: -0.48 (0.39), residues: 184
  loop : -0.98 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 292 
 TYR   0.031   0.002   TYR H 151 
 PHE   0.021   0.002   PHE A 466 
 TRP   0.015   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 7659)
  covalent geometry    : angle       0.64729 (10444)
  SS BOND              : bond        0.00274 (    5)
  SS BOND              : angle       1.09667 (   10)
  hydrogen bonds       : bond        0.03907 (  375)
  hydrogen bonds       : angle       4.95548 ( 1110)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   78 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.6370 (t80)
REVERT: A   97 ILE cc_start: 0.8457 (mm) cc_final: 0.8173 (mt)
REVERT: A  121 CYS cc_start: 0.8788 (OUTLIER) cc_final: 0.7888 (p)
REVERT: A  147 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7734 (t80)
REVERT: A  226 TRP cc_start: 0.7201 (m100) cc_final: 0.6657 (p-90)
REVERT: A  244 TRP cc_start: 0.7897 (t60) cc_final: 0.7604 (t60)
REVERT: A  299 TRP cc_start: 0.8180 (m100) cc_final: 0.7694 (m100)
REVERT: A  339 CYS cc_start: 0.7761 (t) cc_final: 0.6818 (m)
REVERT: A  464 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8437 (tp-100)
REVERT: A  517 MET cc_start: 0.7625 (mmm) cc_final: 0.7295 (mmm)
REVERT: L   11 MET cc_start: 0.6728 (mmt) cc_final: 0.6083 (mmt)
REVERT: L   53 SER cc_start: 0.8471 (m) cc_final: 0.8193 (p)
  outliers start: 17
  outliers final: 13
  residues processed: 137
  average time/residue: 0.0922
  time to fit residues: 16.9705
Evaluate side-chains
  137 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  147 TYR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 THR
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  207 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 74 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
L 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.183406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.146032 restraints weight = 11582.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.150319 restraints weight = 6235.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.153029 restraints weight = 4305.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.154680 restraints weight = 3437.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.155529 restraints weight = 2994.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.177   7664  Z= 0.281
  Angle     :  1.040  59.190  10454  Z= 0.587
  Chirality :  0.051   0.855   1178
  Planarity :  0.004   0.056   1292
  Dihedral  :  4.120  15.877   1039
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 21.78 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.28), residues: 958
  helix:  1.05 (0.27), residues: 387
  sheet: -0.48 (0.39), residues: 184
  loop : -0.98 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 292 
 TYR   0.027   0.002   TYR H 151 
 PHE   0.023   0.002   PHE A 466 
 TRP   0.056   0.003   TRP L 164 
 HIS   0.003   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00590 ( 7659)
  covalent geometry    : angle       1.03956 (10444)
  SS BOND              : bond        0.00266 (    5)
  SS BOND              : angle       1.06787 (   10)
  hydrogen bonds       : bond        0.04005 (  375)
  hydrogen bonds       : angle       4.97636 ( 1110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1446.60 seconds
wall clock time: 25 minutes 44.61 seconds (1544.61 seconds total)