Starting phenix.real_space_refine
on Tue Mar  3 13:15:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6w4s_21539/03_2026/6w4s_21539.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6w4s_21539/03_2026/6w4s_21539.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6w4s_21539/03_2026/6w4s_21539.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6w4s_21539/03_2026/6w4s_21539.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6w4s_21539/03_2026/6w4s_21539.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6w4s_21539/03_2026/6w4s_21539.map"
  }
  resolution = 3.2
  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=  -0.041 sd=   0.719
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    3240      2.51       5
     N     814      2.21       5
     O     903      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4986
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "F"
      Number of atoms: 3216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 3216
          Classifications: {'peptide': 421}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 8, 'TRANS': 412}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "H"
      Number of atoms: 926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 926
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "L"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 844
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 1.29, per 1000 atoms: 0.26
  Number of scatterers: 4986
  At special positions: 0
  Unit cell: (100.158, 98.4608, 92.5192, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O     903      8.00
     N     814      7.00
     C    3240      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  92 " 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: 0.40
  Conformation dependent library (CDL) restraints added in 360.3 milliseconds
  

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1194

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 8 sheets defined
      60.0% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'F' and resid 18 through 23
    Processing helix  chain 'F' and resid 25 through 55
    Processing helix  chain 'F' and resid 57 through 86
      removed outlier: 5.183A  pdb=" N   ALA F  77 " --> pdb=" O   LEU F  73 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   ILE F  78 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LYS F  85 " --> pdb=" O   ASP F  81 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASN F  86 " --> pdb=" O   TRP F  82 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 116
      removed outlier: 3.649A  pdb=" N   ILE F 109 " --> pdb=" O   LEU F 105 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 116 through 123
    Processing helix  chain 'F' and resid 125 through 157
      removed outlier: 4.326A  pdb=" N   LEU F 129 " --> pdb=" O   HIS F 125 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE F 142 " --> pdb=" O   THR F 138 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 157 through 162
      removed outlier: 3.507A  pdb=" N   VAL F 161 " --> pdb=" O   ASP F 157 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 166 through 198
      removed outlier: 4.236A  pdb=" N   LEU F 170 " --> pdb=" O   ASP F 166 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ILE F 186 " --> pdb=" O   GLN F 182 " (cutoff:3.500A)
      Proline residue:  F 189  - end of helix
    Processing helix  chain 'F' and resid 200 through 230
      removed outlier: 3.694A  pdb=" N   GLY F 206 " --> pdb=" O   VAL F 202 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER F 209 " --> pdb=" O   CYS F 205 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 231 through 234
      removed outlier: 3.622A  pdb=" N   ALA F 234 " --> pdb=" O   PRO F 231 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 231 through 234'
    Processing helix  chain 'F' and resid 292 through 304
      removed outlier: 3.694A  pdb=" N   ASN F 304 " --> pdb=" O   VAL F 300 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 307 through 317
      removed outlier: 3.560A  pdb=" N   LEU F 317 " --> pdb=" O   GLY F 313 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 327 through 335
    Processing helix  chain 'F' and resid 338 through 367
    Processing helix  chain 'F' and resid 370 through 393
      removed outlier: 3.903A  pdb=" N   LEU F 374 " --> pdb=" O   VAL F 370 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU F 386 " --> pdb=" O   SER F 382 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   VAL F 391 " --> pdb=" O   CYS F 387 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   PHE F 392 " --> pdb=" O   VAL F 388 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 452 through 484
      removed outlier: 4.547A  pdb=" N   ILE F 467 " --> pdb=" O   ILE F 463 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   GLY F 468 " --> pdb=" O   ALA F 464 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASN F 483 " --> pdb=" O   LEU F 479 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL F 484 " --> pdb=" O   LEU F 480 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 488 through 514
    Processing helix  chain 'F' and resid 516 through 546
      removed outlier: 4.133A  pdb=" N   LEU F 525 " --> pdb=" O   GLY F 521 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.863A  pdb=" N   GLN H  66 " --> pdb=" O   ASN H  83 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.628A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ARG H  38 " --> pdb=" O   TYR H  47 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   TYR H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.389A  pdb=" N   VAL H 107 " --> pdb=" O   ARG H  97 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7
      removed outlier: 3.772A  pdb=" N   CYS L  23 " --> pdb=" O   PHE L  75 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE L  75 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 12 through 13
      removed outlier: 3.736A  pdb=" N   VAL L  13 " --> pdb=" O   GLU L 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'L' and resid 30 through 31
    Processing sheet with id=AA7, first strand: chain 'L' and resid 49 through 52
      removed outlier: 6.855A  pdb=" N   TRP L  39 " --> pdb=" O   LEU L  51 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   THR L 101 " --> pdb=" O   HIS L  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 49 through 52
      removed outlier: 6.855A  pdb=" N   TRP L  39 " --> pdb=" O   LEU L  51 " (cutoff:3.500A)

    372 hydrogen bonds defined for protein.
    1068 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: 0.94

  Time building geometry restraints manager: 0.56 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: 1539
        1.34 -     1.46: 1053
        1.46 -     1.58: 2463
        1.58 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 5101
  Sorted by residual:
  bond pdb=" CA  ASP L  86 "
       pdb=" C   ASP L  86 "
    ideal  model  delta    sigma   weight residual
    1.523  1.499  0.025 1.80e-02 3.09e+03 1.86e+00
  bond pdb=" CG1 ILE H  37 "
       pdb=" CD1 ILE H  37 "
    ideal  model  delta    sigma   weight residual
    1.513  1.479  0.034 3.90e-02 6.57e+02 7.70e-01
  bond pdb=" N   VAL L  62 "
       pdb=" CA  VAL L  62 "
    ideal  model  delta    sigma   weight residual
    1.468  1.460  0.009 1.05e-02 9.07e+03 6.89e-01
  bond pdb=" CB  ASP F 473 "
       pdb=" CG  ASP F 473 "
    ideal  model  delta    sigma   weight residual
    1.516  1.496  0.020 2.50e-02 1.60e+03 6.26e-01
  bond pdb=" CB  ASN L  95 "
       pdb=" CG  ASN L  95 "
    ideal  model  delta    sigma   weight residual
    1.516  1.496  0.020 2.50e-02 1.60e+03 6.09e-01
  ... (remaining 5096 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 6615
        1.16 -     2.33: 276
        2.33 -     3.49: 45
        3.49 -     4.66: 12
        4.66 -     5.82: 4
  Bond angle restraints: 6952
  Sorted by residual:
  angle pdb=" N   ILE F 186 "
        pdb=" CA  ILE F 186 "
        pdb=" C   ILE F 186 "
      ideal   model   delta    sigma   weight residual
     113.42  110.12    3.30 1.17e+00 7.31e-01 7.93e+00
  angle pdb=" C   GLY F  55 "
        pdb=" N   ASN F  56 "
        pdb=" CA  ASN F  56 "
      ideal   model   delta    sigma   weight residual
     121.54  126.50   -4.96 1.91e+00 2.74e-01 6.75e+00
  angle pdb=" C   PHE F 472 "
        pdb=" N   ASP F 473 "
        pdb=" CA  ASP F 473 "
      ideal   model   delta    sigma   weight residual
     120.31  116.82    3.49 1.52e+00 4.33e-01 5.28e+00
  angle pdb=" N   PRO L  50 "
        pdb=" CA  PRO L  50 "
        pdb=" C   PRO L  50 "
      ideal   model   delta    sigma   weight residual
     110.21  113.76   -3.55 1.64e+00 3.72e-01 4.68e+00
  angle pdb=" C   LEU L  54 "
        pdb=" N   ALA L  55 "
        pdb=" CA  ALA L  55 "
      ideal   model   delta    sigma   weight residual
     121.54  125.67   -4.13 1.91e+00 2.74e-01 4.67e+00
  ... (remaining 6947 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.75: 2640
       16.75 -    33.50: 250
       33.50 -    50.25: 46
       50.25 -    66.99: 16
       66.99 -    83.74: 5
  Dihedral angle restraints: 2957
    sinusoidal: 1085
      harmonic: 1872
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  95 "
           pdb=" CB  CYS H  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.54  -43.54     1      1.00e+01 1.00e-02 2.64e+01
  dihedral pdb=" CA  TYR H  50 "
           pdb=" C   TYR H  50 "
           pdb=" N   ILE H  51 "
           pdb=" CA  ILE H  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.76   17.24     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  LEU L  54 "
           pdb=" C   LEU L  54 "
           pdb=" N   ALA L  55 "
           pdb=" CA  ALA L  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.76   16.24     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 2954 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 475
       0.027 -    0.053: 211
       0.053 -    0.080: 89
       0.080 -    0.107: 37
       0.107 -    0.133: 12
  Chirality restraints: 824
  Sorted by residual:
  chirality pdb=" CA  ILE L  52 "
            pdb=" N   ILE L  52 "
            pdb=" C   ILE L  52 "
            pdb=" CB  ILE L  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  ASN F  56 "
            pdb=" N   ASN F  56 "
            pdb=" C   ASN F  56 "
            pdb=" CB  ASN F  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.16e-01
  chirality pdb=" CA  ILE H  37 "
            pdb=" N   ILE H  37 "
            pdb=" C   ILE H  37 "
            pdb=" CB  ILE H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 821 not shown)

  Planarity restraints: 849
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN F 516 "   -0.032 5.00e-02 4.00e+02   4.87e-02 3.79e+00
        pdb=" N   PRO F 517 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO F 517 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO F 517 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L  47 "    0.031 5.00e-02 4.00e+02   4.62e-02 3.42e+00
        pdb=" N   PRO L  48 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO L  48 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO L  48 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H  40 "   -0.022 5.00e-02 4.00e+02   3.36e-02 1.80e+00
        pdb=" N   PRO H  41 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO H  41 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO H  41 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 846 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 267
        2.72 -     3.27: 5211
        3.27 -     3.81: 7917
        3.81 -     4.36: 9283
        4.36 -     4.90: 16708
  Nonbonded interactions: 39386
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F 122 "
            pdb=" O   ARG L  96 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" NE2 GLN L  93 "
            pdb=" OD1 ASN L  95 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OD1 ASN H  60 "
            pdb=" OG  SER H  62 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   VAL F  67 "
            pdb=" OG  SER F  71 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OE2 GLU F 119 "
            pdb=" OH  TYR H  33 "
     model   vdw
     2.260 3.040
  ... (remaining 39381 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.130
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  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:1.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5103  Z= 0.187
  Angle     :  0.571   5.823   6956  Z= 0.331
  Chirality :  0.039   0.133    824
  Planarity :  0.004   0.049    849
  Dihedral  : 14.378  83.741   1757
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 11.87 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole: -1.13 (0.33), residues: 640
  helix:  0.50 (0.27), residues: 371
  sheet: -0.84 (0.53), residues: 100
  loop : -3.49 (0.37), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  40 
 TYR   0.019   0.002   TYR H  78 
 PHE   0.018   0.001   PHE F 295 
 TRP   0.012   0.002   TRP F 470 
 HIS   0.004   0.001   HIS F 507 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 5101)
  covalent geometry    : angle       0.57124 ( 6952)
  SS BOND              : bond        0.00266 (    2)
  SS BOND              : angle       0.47295 (    4)
  hydrogen bonds       : bond        0.13087 (  358)
  hydrogen bonds       : angle       5.96243 ( 1068)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.139 
Fit side-chains
REVERT: F   42 TRP cc_start: 0.8779 (OUTLIER) cc_final: 0.8338 (t-100)
REVERT: F  112 MET cc_start: 0.7755 (mmm) cc_final: 0.7532 (mmm)
REVERT: F  167 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7886 (mmt-90)
REVERT: F  385 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8752 (tt)
REVERT: F  482 GLU cc_start: 0.7658 (tt0) cc_final: 0.7206 (tt0)
REVERT: F  486 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7572 (tm-30)
REVERT: F  540 ARG cc_start: 0.6969 (mtm180) cc_final: 0.6696 (ttt90)
REVERT: L   24 ARG cc_start: 0.7906 (mpp-170) cc_final: 0.7693 (ptt90)
  outliers start: 24
  outliers final: 18
  residues processed: 125
  average time/residue: 0.0683
  time to fit residues: 11.0293
Evaluate side-chains
  111 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 TRP
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  167 ARG
Chi-restraints excluded: chain F residue  215 SER
Chi-restraints excluded: chain F residue  385 ILE
Chi-restraints excluded: chain F residue  473 ASP
Chi-restraints excluded: chain F residue  477 THR
Chi-restraints excluded: chain F residue  484 VAL
Chi-restraints excluded: chain F residue  507 HIS
Chi-restraints excluded: chain F residue  522 LEU
Chi-restraints excluded: chain F residue  527 SER
Chi-restraints excluded: chain F residue  545 THR
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain H residue   67 ILE
Chi-restraints excluded: chain H residue   79 TYR
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 ILE
Chi-restraints excluded: chain L residue   82 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
F  99 GLN
F 141 ASN
F 174 ASN
F 185 ASN
F 481 GLN
F 496 GLN
F 516 ASN
H  16 GLN
H  35 ASN
H  76 ASN
H  77 HIS
L  38 HIS
L  42 GLN
L  78 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.130704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.107001 restraints weight = 7829.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.77
r_work: 0.3188 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5103  Z= 0.159
  Angle     :  0.557   6.458   6956  Z= 0.306
  Chirality :  0.040   0.193    824
  Planarity :  0.005   0.041    849
  Dihedral  :  7.104  58.263    731
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 16.70 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole:  0.45 (0.35), residues: 640
  helix:  1.74 (0.28), residues: 370
  sheet: -0.09 (0.54), residues: 102
  loop : -2.83 (0.40), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 167 
 TYR   0.017   0.002   TYR H  78 
 PHE   0.013   0.001   PHE F 295 
 TRP   0.009   0.001   TRP F 470 
 HIS   0.004   0.001   HIS F 507 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 5101)
  covalent geometry    : angle       0.55713 ( 6952)
  SS BOND              : bond        0.00117 (    2)
  SS BOND              : angle       0.47916 (    4)
  hydrogen bonds       : bond        0.05220 (  358)
  hydrogen bonds       : angle       4.58546 ( 1068)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.182 
Fit side-chains
REVERT: F  385 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8564 (tt)
REVERT: F  474 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7411 (mp)
REVERT: F  540 ARG cc_start: 0.6884 (mtm180) cc_final: 0.6373 (ttm-80)
REVERT: L   24 ARG cc_start: 0.8151 (mpp-170) cc_final: 0.7286 (ptt90)
  outliers start: 27
  outliers final: 17
  residues processed: 121
  average time/residue: 0.0655
  time to fit residues: 10.2890
Evaluate side-chains
  106 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 ASN
Chi-restraints excluded: chain F residue  122 THR
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  162 VAL
Chi-restraints excluded: chain F residue  215 SER
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  385 ILE
Chi-restraints excluded: chain F residue  386 LEU
Chi-restraints excluded: chain F residue  473 ASP
Chi-restraints excluded: chain F residue  474 LEU
Chi-restraints excluded: chain F residue  507 HIS
Chi-restraints excluded: chain F residue  522 LEU
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   67 ILE
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   82 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 57 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 43 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.133458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.110104 restraints weight = 7634.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.74
r_work: 0.3244 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5103  Z= 0.122
  Angle     :  0.529   6.759   6956  Z= 0.282
  Chirality :  0.039   0.139    824
  Planarity :  0.004   0.040    849
  Dihedral  :  6.026  58.623    714
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 18.55 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole:  1.26 (0.35), residues: 640
  helix:  2.35 (0.28), residues: 369
  sheet: -0.09 (0.55), residues: 104
  loop : -2.16 (0.42), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  96 
 TYR   0.016   0.001   TYR H  78 
 PHE   0.011   0.001   PHE F 295 
 TRP   0.012   0.001   TRP F  42 
 HIS   0.003   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 5101)
  covalent geometry    : angle       0.52888 ( 6952)
  SS BOND              : bond        0.00347 (    2)
  SS BOND              : angle       0.34859 (    4)
  hydrogen bonds       : bond        0.04488 (  358)
  hydrogen bonds       : angle       4.27510 ( 1068)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: F  166 ASP cc_start: 0.8228 (t0) cc_final: 0.8009 (t0)
REVERT: F  385 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8427 (tt)
REVERT: F  386 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7471 (tt)
REVERT: F  540 ARG cc_start: 0.6842 (mtm180) cc_final: 0.6343 (ttm-80)
REVERT: L   24 ARG cc_start: 0.8056 (mpp-170) cc_final: 0.7239 (ptt90)
REVERT: L   37 MET cc_start: 0.7902 (tpt) cc_final: 0.7660 (tpt)
  outliers start: 22
  outliers final: 14
  residues processed: 121
  average time/residue: 0.0670
  time to fit residues: 10.6169
Evaluate side-chains
  106 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain F residue   86 ASN
Chi-restraints excluded: chain F residue  162 VAL
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  385 ILE
Chi-restraints excluded: chain F residue  386 LEU
Chi-restraints excluded: chain F residue  473 ASP
Chi-restraints excluded: chain F residue  507 HIS
Chi-restraints excluded: chain F residue  522 LEU
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   67 ILE
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   94 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 46 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.6586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.131463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.108050 restraints weight = 7787.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.71
r_work: 0.3232 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5103  Z= 0.181
  Angle     :  0.575   7.550   6956  Z= 0.306
  Chirality :  0.041   0.170    824
  Planarity :  0.004   0.040    849
  Dihedral  :  6.036  56.280    710
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 20.59 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole:  1.23 (0.35), residues: 640
  helix:  2.09 (0.28), residues: 376
  sheet:  0.29 (0.55), residues: 102
  loop : -1.98 (0.44), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  18 
 TYR   0.020   0.002   TYR H  78 
 PHE   0.016   0.001   PHE F 295 
 TRP   0.013   0.001   TRP F  42 
 HIS   0.005   0.001   HIS F 507 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 5101)
  covalent geometry    : angle       0.57459 ( 6952)
  SS BOND              : bond        0.00119 (    2)
  SS BOND              : angle       0.57309 (    4)
  hydrogen bonds       : bond        0.05218 (  358)
  hydrogen bonds       : angle       4.36792 ( 1068)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.160 
Fit side-chains
REVERT: F  386 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7655 (tt)
REVERT: F  540 ARG cc_start: 0.6946 (mtm180) cc_final: 0.6367 (ttm-80)
REVERT: L   17 GLN cc_start: 0.7801 (tt0) cc_final: 0.7051 (tt0)
REVERT: L   24 ARG cc_start: 0.8146 (mpp-170) cc_final: 0.7368 (ptt90)
REVERT: L   37 MET cc_start: 0.8098 (tpt) cc_final: 0.7703 (tpt)
  outliers start: 24
  outliers final: 17
  residues processed: 111
  average time/residue: 0.0656
  time to fit residues: 9.5846
Evaluate side-chains
  103 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 ASN
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  162 VAL
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  386 LEU
Chi-restraints excluded: chain F residue  507 HIS
Chi-restraints excluded: chain F residue  522 LEU
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   67 ILE
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   94 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 61 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.134841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.111316 restraints weight = 7747.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.76
r_work: 0.3281 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5103  Z= 0.125
  Angle     :  0.540   7.505   6956  Z= 0.285
  Chirality :  0.039   0.168    824
  Planarity :  0.004   0.041    849
  Dihedral  :  5.164  53.475    706
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 21.15 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole:  1.52 (0.35), residues: 640
  helix:  2.32 (0.28), residues: 375
  sheet:  0.31 (0.56), residues: 100
  loop : -1.74 (0.46), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 167 
 TYR   0.015   0.001   TYR H  78 
 PHE   0.011   0.001   PHE F 295 
 TRP   0.013   0.001   TRP F  42 
 HIS   0.003   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5101)
  covalent geometry    : angle       0.54049 ( 6952)
  SS BOND              : bond        0.00238 (    2)
  SS BOND              : angle       0.55870 (    4)
  hydrogen bonds       : bond        0.04506 (  358)
  hydrogen bonds       : angle       4.24513 ( 1068)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: F  312 MET cc_start: 0.8572 (mmm) cc_final: 0.8236 (mmm)
REVERT: F  540 ARG cc_start: 0.6863 (mtm180) cc_final: 0.6329 (ttm-80)
REVERT: H  100 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9082 (mp)
REVERT: L   17 GLN cc_start: 0.7808 (tt0) cc_final: 0.7076 (tt0)
REVERT: L   24 ARG cc_start: 0.8105 (mpp-170) cc_final: 0.7256 (ptt90)
  outliers start: 20
  outliers final: 13
  residues processed: 108
  average time/residue: 0.0638
  time to fit residues: 9.0499
Evaluate side-chains
  101 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain F residue   86 ASN
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  162 VAL
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  522 LEU
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   67 ILE
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   94 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 54 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.133771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.110436 restraints weight = 7800.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.73
r_work: 0.3275 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5103  Z= 0.139
  Angle     :  0.560   8.140   6956  Z= 0.293
  Chirality :  0.040   0.157    824
  Planarity :  0.004   0.040    849
  Dihedral  :  4.978  51.514    704
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 20.04 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole:  1.48 (0.35), residues: 640
  helix:  2.26 (0.28), residues: 374
  sheet:  0.17 (0.55), residues: 104
  loop : -1.59 (0.47), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 167 
 TYR   0.019   0.002   TYR F 133 
 PHE   0.013   0.001   PHE F 295 
 TRP   0.013   0.001   TRP F  42 
 HIS   0.004   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5101)
  covalent geometry    : angle       0.55982 ( 6952)
  SS BOND              : bond        0.00104 (    2)
  SS BOND              : angle       0.67301 (    4)
  hydrogen bonds       : bond        0.04679 (  358)
  hydrogen bonds       : angle       4.24101 ( 1068)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: F  385 ILE cc_start: 0.8239 (tt) cc_final: 0.7681 (pt)
REVERT: F  474 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7710 (mp)
REVERT: F  540 ARG cc_start: 0.6870 (mtm180) cc_final: 0.6336 (ttm-80)
REVERT: L   17 GLN cc_start: 0.7810 (tt0) cc_final: 0.7092 (tt0)
REVERT: L   24 ARG cc_start: 0.8101 (mpp-170) cc_final: 0.7300 (ptt90)
  outliers start: 25
  outliers final: 21
  residues processed: 113
  average time/residue: 0.0604
  time to fit residues: 9.1101
Evaluate side-chains
  109 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   53 LEU
Chi-restraints excluded: chain F residue   86 ASN
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  162 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  474 LEU
Chi-restraints excluded: chain F residue  507 HIS
Chi-restraints excluded: chain F residue  522 LEU
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   67 ILE
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   79 ILE
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   94 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
H  98 GLN
L   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.134002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.110507 restraints weight = 7738.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.74
r_work: 0.3274 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5103  Z= 0.140
  Angle     :  0.590  13.037   6956  Z= 0.301
  Chirality :  0.040   0.166    824
  Planarity :  0.004   0.039    849
  Dihedral  :  4.963  51.471    704
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 20.59 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole:  1.51 (0.35), residues: 640
  helix:  2.25 (0.28), residues: 374
  sheet:  0.18 (0.55), residues: 104
  loop : -1.49 (0.47), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  18 
 TYR   0.017   0.001   TYR H  78 
 PHE   0.012   0.001   PHE F 295 
 TRP   0.013   0.001   TRP F  42 
 HIS   0.003   0.001   HIS F 507 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5101)
  covalent geometry    : angle       0.58951 ( 6952)
  SS BOND              : bond        0.00203 (    2)
  SS BOND              : angle       0.88052 (    4)
  hydrogen bonds       : bond        0.04671 (  358)
  hydrogen bonds       : angle       4.25548 ( 1068)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: F  385 ILE cc_start: 0.8039 (tt) cc_final: 0.7474 (pt)
REVERT: F  474 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7708 (mp)
REVERT: F  540 ARG cc_start: 0.6799 (mtm180) cc_final: 0.6280 (ttm-80)
REVERT: H  100 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9111 (mp)
REVERT: L    6 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7489 (tp40)
REVERT: L    7 SER cc_start: 0.8342 (t) cc_final: 0.7592 (p)
REVERT: L   17 GLN cc_start: 0.7810 (tt0) cc_final: 0.7129 (tt0)
REVERT: L   24 ARG cc_start: 0.8163 (mpp-170) cc_final: 0.7235 (ptt90)
REVERT: L   37 MET cc_start: 0.8006 (tpt) cc_final: 0.7657 (tpt)
  outliers start: 27
  outliers final: 21
  residues processed: 114
  average time/residue: 0.0652
  time to fit residues: 9.8197
Evaluate side-chains
  114 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   53 LEU
Chi-restraints excluded: chain F residue   86 ASN
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  162 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  333 TYR
Chi-restraints excluded: chain F residue  474 LEU
Chi-restraints excluded: chain F residue  507 HIS
Chi-restraints excluded: chain F residue  522 LEU
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   67 ILE
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   94 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.135427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.111614 restraints weight = 7797.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.79
r_work: 0.3284 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5103  Z= 0.127
  Angle     :  0.628  20.870   6956  Z= 0.303
  Chirality :  0.040   0.154    824
  Planarity :  0.004   0.039    849
  Dihedral  :  4.904  51.447    704
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 21.52 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole:  1.61 (0.35), residues: 640
  helix:  2.32 (0.28), residues: 375
  sheet:  0.13 (0.55), residues: 104
  loop : -1.38 (0.48), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  18 
 TYR   0.021   0.001   TYR F 133 
 PHE   0.011   0.001   PHE F 295 
 TRP   0.014   0.001   TRP F  42 
 HIS   0.003   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5101)
  covalent geometry    : angle       0.62784 ( 6952)
  SS BOND              : bond        0.00037 (    2)
  SS BOND              : angle       1.02212 (    4)
  hydrogen bonds       : bond        0.04480 (  358)
  hydrogen bonds       : angle       4.22025 ( 1068)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: F  474 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7726 (mp)
REVERT: F  540 ARG cc_start: 0.6807 (mtm180) cc_final: 0.6279 (ttm-80)
REVERT: L    7 SER cc_start: 0.8355 (t) cc_final: 0.7620 (p)
REVERT: L   24 ARG cc_start: 0.8163 (mpp-170) cc_final: 0.7212 (ptt90)
REVERT: L   80 HIS cc_start: 0.6799 (t70) cc_final: 0.6545 (t70)
REVERT: L  107 LYS cc_start: 0.8361 (tptm) cc_final: 0.8106 (tttt)
REVERT: L  111 LYS cc_start: 0.6320 (mtmt) cc_final: 0.6117 (mtmm)
  outliers start: 26
  outliers final: 22
  residues processed: 113
  average time/residue: 0.0607
  time to fit residues: 9.0340
Evaluate side-chains
  112 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain F residue   53 LEU
Chi-restraints excluded: chain F residue   86 ASN
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  162 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  389 ILE
Chi-restraints excluded: chain F residue  474 LEU
Chi-restraints excluded: chain F residue  507 HIS
Chi-restraints excluded: chain F residue  522 LEU
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   67 ILE
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   94 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 61 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0170
   chunk 10 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.9824

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

Flipped N/Q/H residues before XYZ refinement:
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.134831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.111022 restraints weight = 7804.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.79
r_work: 0.3272 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5103  Z= 0.139
  Angle     :  0.636  18.465   6956  Z= 0.312
  Chirality :  0.041   0.235    824
  Planarity :  0.004   0.039    849
  Dihedral  :  4.937  50.716    704
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 21.34 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole:  1.60 (0.35), residues: 640
  helix:  2.30 (0.27), residues: 375
  sheet:  0.11 (0.54), residues: 104
  loop : -1.33 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  18 
 TYR   0.017   0.001   TYR H  78 
 PHE   0.013   0.001   PHE F 295 
 TRP   0.014   0.001   TRP F  42 
 HIS   0.003   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5101)
  covalent geometry    : angle       0.63577 ( 6952)
  SS BOND              : bond        0.00128 (    2)
  SS BOND              : angle       0.73375 (    4)
  hydrogen bonds       : bond        0.04590 (  358)
  hydrogen bonds       : angle       4.26148 ( 1068)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: F  319 MET cc_start: 0.9172 (tpt) cc_final: 0.8870 (tpt)
REVERT: F  474 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7725 (mp)
REVERT: F  540 ARG cc_start: 0.6820 (mtm180) cc_final: 0.6331 (ttt90)
REVERT: L    7 SER cc_start: 0.8323 (t) cc_final: 0.7588 (p)
REVERT: L   17 GLN cc_start: 0.7741 (tt0) cc_final: 0.7484 (tt0)
REVERT: L   24 ARG cc_start: 0.8145 (mpp-170) cc_final: 0.7218 (ptt90)
REVERT: L   80 HIS cc_start: 0.6803 (t70) cc_final: 0.6489 (t70)
REVERT: L  107 LYS cc_start: 0.8358 (tptm) cc_final: 0.8116 (tttt)
REVERT: L  111 LYS cc_start: 0.6455 (mtmt) cc_final: 0.6244 (mtmm)
  outliers start: 26
  outliers final: 24
  residues processed: 115
  average time/residue: 0.0593
  time to fit residues: 9.0237
Evaluate side-chains
  117 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain F residue   53 LEU
Chi-restraints excluded: chain F residue   86 ASN
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  162 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  333 TYR
Chi-restraints excluded: chain F residue  389 ILE
Chi-restraints excluded: chain F residue  474 LEU
Chi-restraints excluded: chain F residue  507 HIS
Chi-restraints excluded: chain F residue  522 LEU
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   67 ILE
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   79 ILE
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   94 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 54 optimal weight:    7.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** F 174 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 = 0.3717 r_free = 0.3717 target = 0.135840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.112045 restraints weight = 7731.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.78
r_work: 0.3286 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5103  Z= 0.132
  Angle     :  0.630  19.617   6956  Z= 0.309
  Chirality :  0.040   0.209    824
  Planarity :  0.004   0.039    849
  Dihedral  :  4.886  50.955    704
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 21.34 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole:  1.66 (0.35), residues: 640
  helix:  2.35 (0.27), residues: 375
  sheet:  0.09 (0.54), residues: 105
  loop : -1.28 (0.49), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  18 
 TYR   0.016   0.002   TYR H  78 
 PHE   0.012   0.001   PHE F 295 
 TRP   0.014   0.001   TRP F  42 
 HIS   0.003   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5101)
  covalent geometry    : angle       0.63004 ( 6952)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       0.72998 (    4)
  hydrogen bonds       : bond        0.04487 (  358)
  hydrogen bonds       : angle       4.26140 ( 1068)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: F  319 MET cc_start: 0.9172 (tpt) cc_final: 0.8844 (tpt)
REVERT: F  474 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7685 (mp)
REVERT: F  540 ARG cc_start: 0.6784 (mtm180) cc_final: 0.6292 (ttt90)
REVERT: L    7 SER cc_start: 0.8286 (t) cc_final: 0.7589 (p)
REVERT: L   17 GLN cc_start: 0.7748 (tt0) cc_final: 0.7499 (tt0)
REVERT: L   57 ASN cc_start: 0.8730 (m-40) cc_final: 0.8123 (m110)
REVERT: L   80 HIS cc_start: 0.6873 (t70) cc_final: 0.6536 (t70)
REVERT: L  107 LYS cc_start: 0.8361 (tptm) cc_final: 0.8147 (tttt)
REVERT: L  111 LYS cc_start: 0.6357 (mtmt) cc_final: 0.6140 (mtmm)
  outliers start: 25
  outliers final: 23
  residues processed: 113
  average time/residue: 0.0624
  time to fit residues: 9.3406
Evaluate side-chains
  118 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain F residue   53 LEU
Chi-restraints excluded: chain F residue   86 ASN
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  162 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  333 TYR
Chi-restraints excluded: chain F residue  474 LEU
Chi-restraints excluded: chain F residue  507 HIS
Chi-restraints excluded: chain F residue  522 LEU
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   67 ILE
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   79 ILE
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   94 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0050
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
** F 174 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 = 0.3728 r_free = 0.3728 target = 0.136677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.112833 restraints weight = 7710.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.79
r_work: 0.3305 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5103  Z= 0.125
  Angle     :  0.624  19.544   6956  Z= 0.306
  Chirality :  0.041   0.286    824
  Planarity :  0.004   0.039    849
  Dihedral  :  4.747  50.327    704
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 21.34 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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 are not related in a simple way.
  whole:  1.72 (0.35), residues: 640
  helix:  2.40 (0.27), residues: 375
  sheet:  0.09 (0.54), residues: 105
  loop : -1.25 (0.49), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  18 
 TYR   0.016   0.001   TYR H  78 
 PHE   0.011   0.001   PHE F 295 
 TRP   0.014   0.001   TRP F  42 
 HIS   0.003   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5101)
  covalent geometry    : angle       0.62432 ( 6952)
  SS BOND              : bond        0.00147 (    2)
  SS BOND              : angle       0.65156 (    4)
  hydrogen bonds       : bond        0.04351 (  358)
  hydrogen bonds       : angle       4.19987 ( 1068)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1189.78 seconds
wall clock time: 21 minutes 8.44 seconds (1268.44 seconds total)