Starting phenix.real_space_refine
on Tue Mar  3 13:17:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lms_23441/03_2026/7lms_23441.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lms_23441/03_2026/7lms_23441.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lms_23441/03_2026/7lms_23441.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lms_23441/03_2026/7lms_23441.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lms_23441/03_2026/7lms_23441.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lms_23441/03_2026/7lms_23441.cif"
  }
  resolution = 3.5
  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=   0.001 sd=   0.079
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
     Zn      1      6.06       5
     S      24      5.16       5
     C    3149      2.51       5
     N     842      2.21       5
     O     931      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  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: 4947
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1066
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 4, 'TRANS': 133}
    Chain: "A"
      Number of atoms: 3854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3854
          Classifications: {'peptide': 474}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 455}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    391  SG  CYS B  53      49.263  47.066  47.519  1.00 55.77           S
  ATOM    406  SG  CYS B  55      47.370  44.708  48.994  1.00 70.90           S
  ATOM    857  SG  CYS B 113      46.713  48.398  49.288  1.00 47.00           S

  Time building chain proxies: 1.29, per 1000 atoms: 0.26
  Number of scatterers: 4947
  At special positions: 0
  Unit cell: (75.985, 80.995, 93.52, 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)
     Zn      1     29.99
     S      24     16.00
     O     931      8.00
     N     842      7.00
     C    3149      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 334.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 201 "
        pdb="ZN    ZN B 201 " - pdb=" ND1 HIS B 115 "
        pdb="ZN    ZN B 201 " - pdb=" SG  CYS B  55 "
        pdb="ZN    ZN B 201 " - pdb=" SG  CYS B 113 "
        pdb="ZN    ZN B 201 " - pdb=" SG  CYS B  53 "
      Number of angles added : 3


  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1152

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 7 sheets defined
      47.9% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'B' and resid 18 through 20
      No H-bonds generated for 'chain 'B' and resid 18 through 20'
    Processing helix  chain 'B' and resid 21 through 27
    Processing helix  chain 'B' and resid 33 through 35
      No H-bonds generated for 'chain 'B' and resid 33 through 35'
    Processing helix  chain 'B' and resid 103 through 107
    Processing helix  chain 'B' and resid 137 through 141
    Processing helix  chain 'A' and resid 23 through 37
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 45 through 63
      removed outlier: 3.695A  pdb=" N   LYS A  63 " --> pdb=" O   LYS A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 77
    Processing helix  chain 'A' and resid 78 through 88
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 131 through 135
    Processing helix  chain 'A' and resid 139 through 144
    Processing helix  chain 'A' and resid 146 through 152
    Processing helix  chain 'A' and resid 152 through 166
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 185 through 189
    Processing helix  chain 'A' and resid 190 through 195
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 201 through 227
      removed outlier: 4.203A  pdb=" N   ASP A 205 " --> pdb=" O   GLN A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
    Processing helix  chain 'A' and resid 240 through 253
    Processing helix  chain 'A' and resid 317 through 324
    Processing helix  chain 'A' and resid 349 through 360
    Processing helix  chain 'A' and resid 378 through 389
    Processing helix  chain 'A' and resid 391 through 398
    Processing helix  chain 'A' and resid 403 through 409
    Processing helix  chain 'A' and resid 419 through 439
    Processing helix  chain 'A' and resid 444 through 455
    Processing helix  chain 'A' and resid 458 through 494
    Processing sheet with id=AA1, first strand: chain 'B' and resid 7 through 9
      removed outlier: 6.957A  pdb=" N   LEU B  37 " --> pdb=" O   GLU B  31 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   GLU B  31 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   VAL B  39 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 68 through 72
      removed outlier: 3.594A  pdb=" N   PHE B  61 " --> pdb=" O   ILE B 110 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   ILE B 110 " --> pdb=" O   PHE B  61 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLY B 119 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   CYS B 113 " --> pdb=" O   VAL B 117 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   VAL B 117 " --> pdb=" O   CYS B 113 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLY B 130 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   HIS B  94 " --> pdb=" O   ASP B 133 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   GLY B  77 " --> pdb=" O   HIS B  94 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   LEU B  96 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   GLY B  75 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 101
    Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 124
    Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130
    Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 279
      removed outlier: 5.786A  pdb=" N   ASN A 278 " --> pdb=" O   ILE A 311 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 336 through 342

    236 hydrogen bonds defined for protein.
    663 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: 0.64

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1085
        1.32 -     1.45: 1478
        1.45 -     1.58: 2463
        1.58 -     1.70: 1
        1.70 -     1.83: 36
  Bond restraints: 5063
  Sorted by residual:
  bond pdb=" CD  ARG A  75 "
       pdb=" NE  ARG A  75 "
    ideal  model  delta    sigma   weight residual
    1.458  1.398  0.060 1.40e-02 5.10e+03 1.84e+01
  bond pdb=" CD  ARG B  13 "
       pdb=" NE  ARG B  13 "
    ideal  model  delta    sigma   weight residual
    1.458  1.400  0.058 1.40e-02 5.10e+03 1.72e+01
  bond pdb=" CB  PHE A 106 "
       pdb=" CG  PHE A 106 "
    ideal  model  delta    sigma   weight residual
    1.502  1.410  0.092 2.30e-02 1.89e+03 1.59e+01
  bond pdb=" CB  ASN A 154 "
       pdb=" CG  ASN A 154 "
    ideal  model  delta    sigma   weight residual
    1.516  1.417  0.099 2.50e-02 1.60e+03 1.56e+01
  bond pdb=" CB  PHE A 329 "
       pdb=" CG  PHE A 329 "
    ideal  model  delta    sigma   weight residual
    1.502  1.411  0.091 2.30e-02 1.89e+03 1.55e+01
  ... (remaining 5058 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 5648
        1.91 -     3.82: 1020
        3.82 -     5.72: 152
        5.72 -     7.63: 35
        7.63 -     9.54: 2
  Bond angle restraints: 6857
  Sorted by residual:
  angle pdb=" C   TYR B  87 "
        pdb=" N   PRO B  88 "
        pdb=" CA  PRO B  88 "
      ideal   model   delta    sigma   weight residual
     120.21  126.84   -6.63 9.60e-01 1.09e+00 4.77e+01
  angle pdb=" C   SER A  38 "
        pdb=" N   PRO A  39 "
        pdb=" CA  PRO A  39 "
      ideal   model   delta    sigma   weight residual
     120.03  126.73   -6.70 9.90e-01 1.02e+00 4.59e+01
  angle pdb=" C   GLY A 140 "
        pdb=" N   PRO A 141 "
        pdb=" CA  PRO A 141 "
      ideal   model   delta    sigma   weight residual
     119.56  126.11   -6.55 1.02e+00 9.61e-01 4.13e+01
  angle pdb=" C   ALA A  40 "
        pdb=" N   PRO A  41 "
        pdb=" CA  PRO A  41 "
      ideal   model   delta    sigma   weight residual
     120.04  126.84   -6.80 1.08e+00 8.57e-01 3.96e+01
  angle pdb=" C   GLY A  42 "
        pdb=" N   PRO A  43 "
        pdb=" CA  PRO A  43 "
      ideal   model   delta    sigma   weight residual
     119.28  126.18   -6.90 1.10e+00 8.26e-01 3.94e+01
  ... (remaining 6852 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.10: 2849
       14.10 -    28.20: 120
       28.20 -    42.30: 17
       42.30 -    56.39: 10
       56.39 -    70.49: 11
  Dihedral angle restraints: 3007
    sinusoidal: 1217
      harmonic: 1790
  Sorted by residual:
  dihedral pdb=" CA  ARG B 112 "
           pdb=" C   ARG B 112 "
           pdb=" N   CYS B 113 "
           pdb=" CA  CYS B 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.02   20.98     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" C   PHE A 409 "
           pdb=" N   PHE A 409 "
           pdb=" CA  PHE A 409 "
           pdb=" CB  PHE A 409 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.16    8.56     0      2.50e+00 1.60e-01 1.17e+01
  dihedral pdb=" CA  VAL B  15 "
           pdb=" C   VAL B  15 "
           pdb=" N   ASN B  16 "
           pdb=" CA  ASN B  16 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.11   15.89     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 3004 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 381
       0.062 -    0.123: 272
       0.123 -    0.185: 61
       0.185 -    0.247: 24
       0.247 -    0.309: 6
  Chirality restraints: 744
  Sorted by residual:
  chirality pdb=" CA  PHE A  79 "
            pdb=" N   PHE A  79 "
            pdb=" C   PHE A  79 "
            pdb=" CB  PHE A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CA  PHE A 220 "
            pdb=" N   PHE A 220 "
            pdb=" C   PHE A 220 "
            pdb=" CB  PHE A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CA  LYS A 126 "
            pdb=" N   LYS A 126 "
            pdb=" C   LYS A 126 "
            pdb=" CB  LYS A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 741 not shown)

  Planarity restraints: 880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' SAH A 601 "   -0.309 2.00e-02 2.50e+03   1.26e-01 4.34e+02
        pdb=" C2  SAH A 601 "    0.057 2.00e-02 2.50e+03
        pdb=" C4  SAH A 601 "    0.075 2.00e-02 2.50e+03
        pdb=" C5  SAH A 601 "    0.027 2.00e-02 2.50e+03
        pdb=" C6  SAH A 601 "   -0.040 2.00e-02 2.50e+03
        pdb=" C8  SAH A 601 "    0.123 2.00e-02 2.50e+03
        pdb=" N1  SAH A 601 "   -0.020 2.00e-02 2.50e+03
        pdb=" N3  SAH A 601 "    0.092 2.00e-02 2.50e+03
        pdb=" N6  SAH A 601 "   -0.170 2.00e-02 2.50e+03
        pdb=" N7  SAH A 601 "    0.072 2.00e-02 2.50e+03
        pdb=" N9  SAH A 601 "    0.094 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  85 "   -0.075 2.00e-02 2.50e+03   3.58e-02 3.21e+01
        pdb=" CG  TRP A  85 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  85 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  85 "    0.038 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  85 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  85 "    0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  85 "    0.044 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  85 "   -0.037 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  85 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  85 "   -0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 344 "   -0.015 2.00e-02 2.50e+03   2.92e-02 8.52e+00
        pdb=" C   SER A 344 "    0.050 2.00e-02 2.50e+03
        pdb=" O   SER A 344 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LYS A 345 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 877 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 2263
        2.93 -     3.42: 4742
        3.42 -     3.91: 8329
        3.91 -     4.41: 9594
        4.41 -     4.90: 15290
  Nonbonded interactions: 40218
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 288 "
            pdb=" OD1 ASP A 293 "
     model   vdw
     2.432 3.040
  nonbonded pdb=" N   ASP A  72 "
            pdb=" OD1 ASP A  72 "
     model   vdw
     2.466 3.120
  nonbonded pdb=" OD1 ASP A 347 "
            pdb=" N   ARG A 348 "
     model   vdw
     2.489 3.120
  nonbonded pdb=" N   ASN A 154 "
            pdb=" OD1 ASN A 154 "
     model   vdw
     2.506 3.120
  nonbonded pdb=" NZ  LYS A  84 "
            pdb=" OE2 GLU A  88 "
     model   vdw
     2.508 3.120
  ... (remaining 40213 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:             1.490
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.290
  Find NCS groups from input model:        0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
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      :  0.020   0.230   5067  Z= 1.090
  Angle     :  1.535  11.680   6860  Z= 1.038
  Chirality :  0.085   0.309    744
  Planarity :  0.009   0.126    880
  Dihedral  : 10.075  70.493   1855
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 0.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.57 (0.31), residues: 608
  helix:  0.26 (0.29), residues: 259
  sheet: -0.63 (0.55), residues: 85
  loop :  1.18 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 215 
 TYR   0.036   0.004   TYR B  60 
 PHE   0.029   0.005   PHE A 368 
 TRP   0.075   0.008   TRP A  85 
 HIS   0.006   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.01925 ( 5063)
  covalent geometry    : angle       1.52073 ( 6857)
  hydrogen bonds       : bond        0.17098 (  236)
  hydrogen bonds       : angle       6.51730 (  663)
  metal coordination   : bond        0.15996 (    4)
  metal coordination   : angle      10.11120 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.7795 (ttt-90) cc_final: 0.7543 (ttm-80)
REVERT: B   80 GLU cc_start: 0.8326 (tt0) cc_final: 0.7970 (tt0)
REVERT: A  276 MET cc_start: 0.8548 (mmm) cc_final: 0.7855 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0876
  time to fit residues: 17.3845
Evaluate side-chains
  83 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B  16 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 = 0.3495 r_free = 0.3495 target = 0.112656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.087351 restraints weight = 7801.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.092292 restraints weight = 3514.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.095633 restraints weight = 2066.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.097824 restraints weight = 1420.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.099308 restraints weight = 1084.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5067  Z= 0.140
  Angle     :  0.589   7.313   6860  Z= 0.309
  Chirality :  0.043   0.180    744
  Planarity :  0.004   0.038    880
  Dihedral  :  4.452  15.922    674
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  :  9.59 %
    Favored  : 88.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.59 (0.33), residues: 608
  helix:  1.85 (0.32), residues: 258
  sheet: -0.79 (0.55), residues: 81
  loop :  1.09 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 336 
 TYR   0.017   0.002   TYR B  86 
 PHE   0.025   0.002   PHE A 159 
 TRP   0.010   0.001   TRP A  85 
 HIS   0.002   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 5063)
  covalent geometry    : angle       0.57534 ( 6857)
  hydrogen bonds       : bond        0.05067 (  236)
  hydrogen bonds       : angle       4.23234 (  663)
  metal coordination   : bond        0.01274 (    4)
  metal coordination   : angle       5.95402 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8352 (ttt-90) cc_final: 0.7923 (ttt90)
REVERT: B   52 ARG cc_start: 0.8713 (mmt-90) cc_final: 0.8064 (mmp80)
REVERT: B   66 ASN cc_start: 0.8586 (t0) cc_final: 0.8358 (t0)
REVERT: B  111 LEU cc_start: 0.8345 (tt) cc_final: 0.8141 (tt)
REVERT: A  320 GLU cc_start: 0.8107 (tt0) cc_final: 0.7697 (tt0)
REVERT: A  340 LYS cc_start: 0.8721 (tttt) cc_final: 0.8507 (tptm)
REVERT: A  352 MET cc_start: 0.8766 (mtp) cc_final: 0.8285 (mtp)
REVERT: A  397 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8577 (mm-30)
REVERT: A  423 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7510 (mm-30)
  outliers start: 12
  outliers final: 5
  residues processed: 107
  average time/residue: 0.0624
  time to fit residues: 8.8142
Evaluate side-chains
  83 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  426 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 209 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.105914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.081014 restraints weight = 8061.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.085516 restraints weight = 3729.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.088548 restraints weight = 2253.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.090597 restraints weight = 1582.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.091988 restraints weight = 1221.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5067  Z= 0.205
  Angle     :  0.611   9.761   6860  Z= 0.317
  Chirality :  0.044   0.202    744
  Planarity :  0.004   0.032    880
  Dihedral  :  4.440  15.994    674
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  :  9.40 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.35 (0.34), residues: 608
  helix:  1.83 (0.33), residues: 265
  sheet: -1.18 (0.56), residues: 73
  loop :  0.74 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.032   0.002   TYR B  86 
 PHE   0.021   0.002   PHE A 159 
 TRP   0.013   0.001   TRP A 122 
 HIS   0.006   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 5063)
  covalent geometry    : angle       0.59792 ( 6857)
  hydrogen bonds       : bond        0.05226 (  236)
  hydrogen bonds       : angle       4.22309 (  663)
  metal coordination   : bond        0.01608 (    4)
  metal coordination   : angle       5.99817 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8296 (ttt-90) cc_final: 0.7275 (ttt90)
REVERT: B   52 ARG cc_start: 0.8884 (mmt-90) cc_final: 0.8320 (mpt180)
REVERT: B   66 ASN cc_start: 0.8558 (t0) cc_final: 0.8296 (t0)
REVERT: B  141 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6834 (mt-10)
REVERT: A  117 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7543 (tm-30)
REVERT: A  147 ARG cc_start: 0.8740 (mmm160) cc_final: 0.8371 (mmm160)
REVERT: A  183 TYR cc_start: 0.8060 (m-80) cc_final: 0.7810 (m-80)
REVERT: A  320 GLU cc_start: 0.8297 (tt0) cc_final: 0.7917 (tt0)
REVERT: A  340 LYS cc_start: 0.8801 (tttt) cc_final: 0.8475 (tptm)
REVERT: A  352 MET cc_start: 0.9054 (mtp) cc_final: 0.8686 (ttm)
REVERT: A  423 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7427 (mm-30)
  outliers start: 19
  outliers final: 14
  residues processed: 99
  average time/residue: 0.0607
  time to fit residues: 8.0141
Evaluate side-chains
  93 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  426 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.109245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.084669 restraints weight = 7876.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.089283 restraints weight = 3556.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.092412 restraints weight = 2102.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.094469 restraints weight = 1452.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.095933 restraints weight = 1120.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.4426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5067  Z= 0.119
  Angle     :  0.516   7.575   6860  Z= 0.268
  Chirality :  0.042   0.201    744
  Planarity :  0.004   0.037    880
  Dihedral  :  4.047  15.711    674
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 11.47 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 (0.34), residues: 608
  helix:  2.11 (0.33), residues: 265
  sheet: -1.11 (0.53), residues: 81
  loop :  0.71 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  89 
 TYR   0.016   0.001   TYR B  86 
 PHE   0.011   0.001   PHE A 159 
 TRP   0.009   0.001   TRP A 122 
 HIS   0.002   0.001   HIS B  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 5063)
  covalent geometry    : angle       0.50613 ( 6857)
  hydrogen bonds       : bond        0.04036 (  236)
  hydrogen bonds       : angle       3.78299 (  663)
  metal coordination   : bond        0.01123 (    4)
  metal coordination   : angle       4.81890 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8346 (ttt-90) cc_final: 0.7367 (ttt90)
REVERT: B   52 ARG cc_start: 0.8869 (mmt-90) cc_final: 0.8651 (mpt180)
REVERT: B   66 ASN cc_start: 0.8586 (t0) cc_final: 0.8281 (t0)
REVERT: B   80 GLU cc_start: 0.8767 (tt0) cc_final: 0.8440 (tt0)
REVERT: B  111 LEU cc_start: 0.8401 (tt) cc_final: 0.8086 (tt)
REVERT: A  117 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7360 (tm-30)
REVERT: A  147 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8346 (mmm160)
REVERT: A  183 TYR cc_start: 0.8050 (m-80) cc_final: 0.7810 (m-80)
REVERT: A  243 ASP cc_start: 0.9007 (t0) cc_final: 0.8794 (t70)
REVERT: A  276 MET cc_start: 0.7447 (mmt) cc_final: 0.7015 (mmm)
REVERT: A  320 GLU cc_start: 0.8294 (tt0) cc_final: 0.7912 (tt0)
REVERT: A  340 LYS cc_start: 0.8808 (tttt) cc_final: 0.8504 (tptm)
REVERT: A  352 MET cc_start: 0.9066 (mtp) cc_final: 0.8663 (mtp)
REVERT: A  397 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8484 (pt0)
REVERT: A  423 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7385 (mm-30)
  outliers start: 15
  outliers final: 12
  residues processed: 98
  average time/residue: 0.0623
  time to fit residues: 8.1408
Evaluate side-chains
  95 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  426 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 4 optimal weight:    0.1980
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    0.1980
   chunk 55 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.116685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.091475 restraints weight = 7980.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.096365 restraints weight = 3625.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.099596 restraints weight = 2154.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.101784 restraints weight = 1499.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.103120 restraints weight = 1154.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.4666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5067  Z= 0.104
  Angle     :  0.490   6.558   6860  Z= 0.254
  Chirality :  0.041   0.180    744
  Planarity :  0.003   0.033    880
  Dihedral  :  3.811  16.756    674
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.16 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 (0.34), residues: 608
  helix:  2.30 (0.34), residues: 264
  sheet: -1.26 (0.52), residues: 83
  loop :  0.57 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  89 
 TYR   0.016   0.001   TYR A 244 
 PHE   0.011   0.001   PHE B 101 
 TRP   0.008   0.001   TRP A 122 
 HIS   0.002   0.000   HIS B  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 5063)
  covalent geometry    : angle       0.48224 ( 6857)
  hydrogen bonds       : bond        0.03627 (  236)
  hydrogen bonds       : angle       3.57703 (  663)
  metal coordination   : bond        0.01077 (    4)
  metal coordination   : angle       4.19629 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8352 (ttt-90) cc_final: 0.7416 (ttt90)
REVERT: B   52 ARG cc_start: 0.8949 (mmt-90) cc_final: 0.8585 (mpt180)
REVERT: B   66 ASN cc_start: 0.8576 (t0) cc_final: 0.8263 (t0)
REVERT: B   80 GLU cc_start: 0.8767 (tt0) cc_final: 0.8317 (tt0)
REVERT: B  111 LEU cc_start: 0.8406 (tt) cc_final: 0.8074 (tt)
REVERT: A   46 GLU cc_start: 0.6736 (tp30) cc_final: 0.6499 (tp30)
REVERT: A  147 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8302 (mmm160)
REVERT: A  207 PHE cc_start: 0.7883 (m-80) cc_final: 0.7228 (m-10)
REVERT: A  276 MET cc_start: 0.7328 (mmt) cc_final: 0.7049 (mmm)
REVERT: A  320 GLU cc_start: 0.8243 (tt0) cc_final: 0.7894 (tt0)
REVERT: A  340 LYS cc_start: 0.8806 (tttt) cc_final: 0.8521 (tptm)
REVERT: A  352 MET cc_start: 0.9064 (mtp) cc_final: 0.8714 (ttm)
REVERT: A  397 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8502 (pt0)
REVERT: A  423 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7397 (mm-30)
  outliers start: 10
  outliers final: 9
  residues processed: 96
  average time/residue: 0.0620
  time to fit residues: 7.9764
Evaluate side-chains
  91 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  426 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0570
   chunk 56 optimal weight:    7.9990
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.3564 r_free = 0.3564 target = 0.117179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.091976 restraints weight = 7991.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.096847 restraints weight = 3622.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.100062 restraints weight = 2142.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.102205 restraints weight = 1486.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.103617 restraints weight = 1149.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.4815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5067  Z= 0.106
  Angle     :  0.488   7.192   6860  Z= 0.254
  Chirality :  0.041   0.220    744
  Planarity :  0.003   0.030    880
  Dihedral  :  3.745  15.608    674
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.47 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.50 (0.35), residues: 608
  helix:  2.31 (0.34), residues: 264
  sheet: -1.35 (0.52), residues: 83
  loop :  0.55 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  89 
 TYR   0.011   0.001   TYR B  86 
 PHE   0.015   0.001   PHE B 101 
 TRP   0.008   0.001   TRP A 122 
 HIS   0.002   0.001   HIS B  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 5063)
  covalent geometry    : angle       0.48086 ( 6857)
  hydrogen bonds       : bond        0.03548 (  236)
  hydrogen bonds       : angle       3.58152 (  663)
  metal coordination   : bond        0.00990 (    4)
  metal coordination   : angle       3.91044 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8381 (ttt-90) cc_final: 0.7427 (ttt90)
REVERT: B   52 ARG cc_start: 0.9001 (mmt-90) cc_final: 0.8574 (mmp80)
REVERT: B   66 ASN cc_start: 0.8560 (t0) cc_final: 0.8234 (t0)
REVERT: B   80 GLU cc_start: 0.8744 (tt0) cc_final: 0.8311 (tt0)
REVERT: B  111 LEU cc_start: 0.8411 (tt) cc_final: 0.8063 (tt)
REVERT: A   24 GLU cc_start: 0.7595 (mp0) cc_final: 0.7390 (tp30)
REVERT: A   46 GLU cc_start: 0.6684 (tp30) cc_final: 0.6458 (tp30)
REVERT: A  147 ARG cc_start: 0.8606 (mmm160) cc_final: 0.8298 (mmm160)
REVERT: A  207 PHE cc_start: 0.7879 (m-80) cc_final: 0.7251 (m-10)
REVERT: A  276 MET cc_start: 0.7241 (mmt) cc_final: 0.6995 (mmm)
REVERT: A  320 GLU cc_start: 0.8240 (tt0) cc_final: 0.7874 (tt0)
REVERT: A  340 LYS cc_start: 0.8796 (tttt) cc_final: 0.8517 (tptm)
REVERT: A  352 MET cc_start: 0.9033 (mtp) cc_final: 0.8715 (ttm)
REVERT: A  397 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8497 (pt0)
REVERT: A  423 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7393 (mm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 96
  average time/residue: 0.0617
  time to fit residues: 7.9357
Evaluate side-chains
  95 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  426 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  54 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.115397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.090191 restraints weight = 7948.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.094979 restraints weight = 3656.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.098118 restraints weight = 2183.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.100251 restraints weight = 1530.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.101697 restraints weight = 1183.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.4890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5067  Z= 0.124
  Angle     :  0.508   6.951   6860  Z= 0.262
  Chirality :  0.042   0.210    744
  Planarity :  0.003   0.030    880
  Dihedral  :  3.749  17.286    674
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.35 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.46 (0.35), residues: 608
  helix:  2.34 (0.34), residues: 265
  sheet: -1.42 (0.52), residues: 83
  loop :  0.49 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  89 
 TYR   0.010   0.001   TYR B  86 
 PHE   0.014   0.001   PHE A 159 
 TRP   0.010   0.001   TRP A 122 
 HIS   0.002   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 5063)
  covalent geometry    : angle       0.50076 ( 6857)
  hydrogen bonds       : bond        0.03768 (  236)
  hydrogen bonds       : angle       3.58617 (  663)
  metal coordination   : bond        0.01046 (    4)
  metal coordination   : angle       4.15063 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8378 (ttt-90) cc_final: 0.8025 (ttt90)
REVERT: B   52 ARG cc_start: 0.9015 (mmt-90) cc_final: 0.8661 (mpt180)
REVERT: B   66 ASN cc_start: 0.8535 (t0) cc_final: 0.8247 (t0)
REVERT: B   80 GLU cc_start: 0.8745 (tt0) cc_final: 0.8374 (tt0)
REVERT: B  111 LEU cc_start: 0.8378 (tt) cc_final: 0.7998 (tt)
REVERT: A   46 GLU cc_start: 0.6779 (tp30) cc_final: 0.6569 (tp30)
REVERT: A  147 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8348 (mmm160)
REVERT: A  162 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7711 (mp)
REVERT: A  207 PHE cc_start: 0.7922 (m-80) cc_final: 0.7305 (m-10)
REVERT: A  276 MET cc_start: 0.7193 (mmt) cc_final: 0.6846 (mmm)
REVERT: A  320 GLU cc_start: 0.8250 (tt0) cc_final: 0.7866 (tt0)
REVERT: A  340 LYS cc_start: 0.8784 (tttt) cc_final: 0.8500 (tptm)
REVERT: A  352 MET cc_start: 0.9089 (mtp) cc_final: 0.8792 (ttm)
REVERT: A  397 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8481 (pt0)
REVERT: A  423 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7388 (mm-30)
REVERT: A  493 MET cc_start: 0.7317 (tpp) cc_final: 0.7076 (tpp)
  outliers start: 17
  outliers final: 16
  residues processed: 95
  average time/residue: 0.0565
  time to fit residues: 7.1492
Evaluate side-chains
  100 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  415 GLU
Chi-restraints excluded: chain A residue  426 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
B  54 GLN
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 GLN ** 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 = 0.3375 r_free = 0.3375 target = 0.104149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.079235 restraints weight = 8320.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.083618 restraints weight = 3869.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.086546 restraints weight = 2354.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.088543 restraints weight = 1666.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.089943 restraints weight = 1300.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.4930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   5067  Z= 0.253
  Angle     :  0.637   8.914   6860  Z= 0.331
  Chirality :  0.045   0.216    744
  Planarity :  0.004   0.034    880
  Dihedral  :  4.341  23.774    674
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 13.16 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.10 (0.35), residues: 608
  helix:  2.04 (0.33), residues: 264
  sheet: -1.63 (0.52), residues: 87
  loop :  0.36 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  89 
 TYR   0.014   0.002   TYR A 188 
 PHE   0.011   0.002   PHE A  79 
 TRP   0.017   0.001   TRP A 122 
 HIS   0.007   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 ( 5063)
  covalent geometry    : angle       0.62762 ( 6857)
  hydrogen bonds       : bond        0.05057 (  236)
  hydrogen bonds       : angle       4.12733 (  663)
  metal coordination   : bond        0.01402 (    4)
  metal coordination   : angle       5.16454 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8431 (ttt-90) cc_final: 0.7507 (ttm-80)
REVERT: B   52 ARG cc_start: 0.9014 (mmt-90) cc_final: 0.8627 (mmp80)
REVERT: B   66 ASN cc_start: 0.8557 (t0) cc_final: 0.8347 (t0)
REVERT: B   80 GLU cc_start: 0.8724 (tt0) cc_final: 0.8145 (tt0)
REVERT: B  135 ARG cc_start: 0.8753 (mtm180) cc_final: 0.8490 (mtp180)
REVERT: A   24 GLU cc_start: 0.7105 (tp30) cc_final: 0.6808 (mt-10)
REVERT: A  147 ARG cc_start: 0.8626 (mmm160) cc_final: 0.8308 (mmm160)
REVERT: A  162 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7933 (mp)
REVERT: A  320 GLU cc_start: 0.8356 (tt0) cc_final: 0.7998 (tt0)
REVERT: A  340 LYS cc_start: 0.8839 (tttt) cc_final: 0.8543 (tptm)
REVERT: A  352 MET cc_start: 0.9110 (mtp) cc_final: 0.8781 (ttm)
REVERT: A  397 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8531 (pt0)
REVERT: A  423 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7427 (mm-30)
  outliers start: 21
  outliers final: 16
  residues processed: 92
  average time/residue: 0.0747
  time to fit residues: 8.7471
Evaluate side-chains
  94 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  415 GLU
Chi-restraints excluded: chain A residue  426 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 17 optimal weight:    0.3980
   chunk 51 optimal weight:    0.1980
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3417 r_free = 0.3417 target = 0.107156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.082602 restraints weight = 8061.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.087053 restraints weight = 3744.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.090039 restraints weight = 2261.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.092067 restraints weight = 1588.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.093449 restraints weight = 1231.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.5055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5067  Z= 0.138
  Angle     :  0.554   8.979   6860  Z= 0.282
  Chirality :  0.042   0.184    744
  Planarity :  0.003   0.030    880
  Dihedral  :  4.028  19.423    674
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 13.16 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.28 (0.35), residues: 608
  helix:  2.27 (0.34), residues: 265
  sheet: -1.71 (0.53), residues: 81
  loop :  0.35 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  89 
 TYR   0.013   0.001   TYR A 188 
 PHE   0.012   0.001   PHE B 101 
 TRP   0.010   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 455 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5063)
  covalent geometry    : angle       0.54390 ( 6857)
  hydrogen bonds       : bond        0.04079 (  236)
  hydrogen bonds       : angle       3.71681 (  663)
  metal coordination   : bond        0.01019 (    4)
  metal coordination   : angle       4.97488 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8398 (ttt-90) cc_final: 0.7423 (ttm-80)
REVERT: B   52 ARG cc_start: 0.9009 (mmt-90) cc_final: 0.8616 (mmp80)
REVERT: B   66 ASN cc_start: 0.8478 (t0) cc_final: 0.8275 (t0)
REVERT: B   80 GLU cc_start: 0.8760 (tt0) cc_final: 0.8424 (tt0)
REVERT: B  111 LEU cc_start: 0.8428 (tt) cc_final: 0.8164 (tt)
REVERT: A  147 ARG cc_start: 0.8678 (mmm160) cc_final: 0.8334 (mmm160)
REVERT: A  162 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7710 (mp)
REVERT: A  207 PHE cc_start: 0.7932 (m-80) cc_final: 0.7591 (m-10)
REVERT: A  276 MET cc_start: 0.7240 (mmt) cc_final: 0.6834 (mmm)
REVERT: A  320 GLU cc_start: 0.8300 (tt0) cc_final: 0.7922 (tt0)
REVERT: A  340 LYS cc_start: 0.8784 (tttt) cc_final: 0.8512 (tptm)
REVERT: A  352 MET cc_start: 0.9111 (mtp) cc_final: 0.8840 (ttm)
REVERT: A  397 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8474 (tp30)
REVERT: A  423 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7410 (mm-30)
  outliers start: 18
  outliers final: 16
  residues processed: 93
  average time/residue: 0.0739
  time to fit residues: 8.9126
Evaluate side-chains
  93 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  415 GLU
Chi-restraints excluded: chain A residue  426 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 30 optimal weight:    0.0980
   chunk 50 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 17 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 23 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 455 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.110684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.085564 restraints weight = 7955.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.090202 restraints weight = 3608.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.093336 restraints weight = 2156.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.095449 restraints weight = 1502.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.096914 restraints weight = 1157.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.5213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5067  Z= 0.110
  Angle     :  0.548   9.311   6860  Z= 0.277
  Chirality :  0.042   0.195    744
  Planarity :  0.003   0.030    880
  Dihedral  :  3.774  15.808    674
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.10 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.44 (0.35), residues: 608
  helix:  2.48 (0.34), residues: 265
  sheet: -1.75 (0.51), residues: 85
  loop :  0.44 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  89 
 TYR   0.011   0.001   TYR A 188 
 PHE   0.013   0.001   PHE B 101 
 TRP   0.007   0.001   TRP A 122 
 HIS   0.004   0.001   HIS A 455 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 5063)
  covalent geometry    : angle       0.54165 ( 6857)
  hydrogen bonds       : bond        0.03616 (  236)
  hydrogen bonds       : angle       3.54957 (  663)
  metal coordination   : bond        0.00851 (    4)
  metal coordination   : angle       4.06785 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8473 (ttt-90) cc_final: 0.7539 (ttm-80)
REVERT: B   52 ARG cc_start: 0.9031 (mmt-90) cc_final: 0.8729 (mmp80)
REVERT: B   66 ASN cc_start: 0.8526 (t0) cc_final: 0.8295 (t0)
REVERT: B   80 GLU cc_start: 0.8786 (tt0) cc_final: 0.8367 (tt0)
REVERT: B  111 LEU cc_start: 0.8494 (tt) cc_final: 0.8141 (tt)
REVERT: A   28 LEU cc_start: 0.7414 (mt) cc_final: 0.6998 (mp)
REVERT: A  162 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7766 (mp)
REVERT: A  207 PHE cc_start: 0.7982 (m-80) cc_final: 0.7664 (m-10)
REVERT: A  276 MET cc_start: 0.7164 (mmt) cc_final: 0.6791 (mmm)
REVERT: A  320 GLU cc_start: 0.8293 (tt0) cc_final: 0.7924 (tt0)
REVERT: A  340 LYS cc_start: 0.8811 (tttt) cc_final: 0.8532 (tptm)
REVERT: A  397 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8563 (pt0)
REVERT: A  423 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7398 (mm-30)
  outliers start: 15
  outliers final: 12
  residues processed: 91
  average time/residue: 0.0600
  time to fit residues: 7.2859
Evaluate side-chains
  91 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  426 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0470
   chunk 53 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.1484

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

Flipped N/Q/H residues before XYZ refinement:
B  92 GLN
A 455 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.104235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.079764 restraints weight = 8273.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.083890 restraints weight = 3980.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.086723 restraints weight = 2454.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.088555 restraints weight = 1747.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.089954 restraints weight = 1378.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.5144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5067  Z= 0.146
  Angle     :  0.567   9.082   6860  Z= 0.289
  Chirality :  0.043   0.189    744
  Planarity :  0.004   0.029    880
  Dihedral  :  3.910  19.367    674
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.10 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.37 (0.35), residues: 608
  helix:  2.42 (0.34), residues: 265
  sheet: -1.70 (0.53), residues: 81
  loop :  0.32 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  89 
 TYR   0.012   0.001   TYR A 188 
 PHE   0.012   0.001   PHE B 101 
 TRP   0.012   0.001   TRP A 122 
 HIS   0.004   0.001   HIS A 455 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 5063)
  covalent geometry    : angle       0.55928 ( 6857)
  hydrogen bonds       : bond        0.04041 (  236)
  hydrogen bonds       : angle       3.69030 (  663)
  metal coordination   : bond        0.01103 (    4)
  metal coordination   : angle       4.55727 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 922.72 seconds
wall clock time: 16 minutes 36.94 seconds (996.94 seconds total)