Starting phenix.real_space_refine
on Tue Feb 11 09:13:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lms_23441/02_2025/7lms_23441.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lms_23441/02_2025/7lms_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_23441/02_2025/7lms_23441.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lms_23441/02_2025/7lms_23441.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lms_23441/02_2025/7lms_23441.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lms_23441/02_2025/7lms_23441.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.60, per 1000 atoms: 0.73
  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: 1.31
  Conformation dependent library (CDL) restraints added in 583.4 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
      47.8% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  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: 1.43

  Time building geometry restraints manager: 1.49 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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.720
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.000
-------------------------------------------------------------------------------
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      :  0.019   0.107   5063  Z= 1.245
  Angle     :  1.521   9.540   6857  Z= 1.037
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (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
 TRP   0.075   0.008   TRP A  85 
 HIS   0.006   0.001   HIS B  68 
 PHE   0.029   0.005   PHE A 368 
 TYR   0.036   0.004   TYR B  60 
 ARG   0.007   0.001   ARG A 215 

*********************** 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  : 0.577 
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: 0.7545 (ttm-80)
REVERT: B   80 GLU cc_start: 0.8326 (tt0) cc_final: 0.7965 (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: 0.2097
  time to fit residues: 41.3102
Evaluate side-chains
  82 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3604 r_free = 0.3604 target = 0.120531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.096053 restraints weight = 7417.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.101002 restraints weight = 3329.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.104283 restraints weight = 1951.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5063  Z= 0.195
  Angle     :  0.577   6.201   6857  Z= 0.309
  Chirality :  0.043   0.177    744
  Planarity :  0.004   0.034    880
  Dihedral  :  4.474  16.475    674
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  :  9.21 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.34), residues: 608
  helix:  1.87 (0.33), residues: 260
  sheet: -0.76 (0.55), residues: 81
  loop :  1.09 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  85 
 HIS   0.003   0.001   HIS B  45 
 PHE   0.023   0.002   PHE A 159 
 TYR   0.020   0.002   TYR B  86 
 ARG   0.003   0.001   ARG A 336 

*********************** 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
  116 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.7351 (ttm170)
REVERT: B   52 ARG cc_start: 0.8709 (mmt-90) cc_final: 0.8261 (mmp80)
REVERT: B  111 LEU cc_start: 0.8248 (tt) cc_final: 0.8023 (tt)
REVERT: A  320 GLU cc_start: 0.8036 (tt0) cc_final: 0.7596 (tt0)
REVERT: A  340 LYS cc_start: 0.8689 (tttt) cc_final: 0.8462 (tptm)
REVERT: A  352 MET cc_start: 0.8783 (mtp) cc_final: 0.8271 (mtp)
REVERT: A  397 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8566 (mm-30)
REVERT: A  423 GLU cc_start: 0.7730 (tp30) cc_final: 0.7338 (tp30)
REVERT: A  476 GLU cc_start: 0.7709 (tt0) cc_final: 0.7479 (tm-30)
  outliers start: 12
  outliers final: 5
  residues processed: 106
  average time/residue: 0.1676
  time to fit residues: 23.2490
Evaluate side-chains
  85 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
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  138 VAL
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 58 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0170
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    0.3980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A 209 GLN
A 380 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.112717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.087921 restraints weight = 7787.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.092776 restraints weight = 3511.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.096120 restraints weight = 2064.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5063  Z= 0.163
  Angle     :  0.521   6.624   6857  Z= 0.274
  Chirality :  0.042   0.198    744
  Planarity :  0.003   0.034    880
  Dihedral  :  4.066  14.071    674
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  :  8.83 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.34), residues: 608
  helix:  2.23 (0.33), residues: 259
  sheet: -0.97 (0.54), residues: 85
  loop :  0.92 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 122 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.015   0.002   PHE A 159 
 TYR   0.026   0.002   TYR B  86 
 ARG   0.003   0.000   ARG A  61 

*********************** 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: 15
    poor density    : 92
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8326 (ttt-90) cc_final: 0.7342 (ttm170)
REVERT: B   52 ARG cc_start: 0.8715 (mmt-90) cc_final: 0.8158 (mpt180)
REVERT: B   80 GLU cc_start: 0.8417 (tt0) cc_final: 0.8159 (tt0)
REVERT: B   91 TYR cc_start: 0.7682 (m-80) cc_final: 0.7430 (m-80)
REVERT: B  101 PHE cc_start: 0.8715 (m-80) cc_final: 0.8425 (m-80)
REVERT: B  111 LEU cc_start: 0.8420 (tt) cc_final: 0.8165 (tt)
REVERT: B  114 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8310 (mp0)
REVERT: A  183 TYR cc_start: 0.8058 (m-80) cc_final: 0.7849 (m-80)
REVERT: A  243 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8667 (t0)
REVERT: A  320 GLU cc_start: 0.8163 (tt0) cc_final: 0.7740 (tt0)
REVERT: A  340 LYS cc_start: 0.8767 (tttt) cc_final: 0.8490 (tptm)
REVERT: A  352 MET cc_start: 0.8978 (mtp) cc_final: 0.8618 (mtp)
REVERT: A  423 GLU cc_start: 0.7778 (tp30) cc_final: 0.7410 (tp30)
  outliers start: 15
  outliers final: 8
  residues processed: 97
  average time/residue: 0.1585
  time to fit residues: 20.6684
Evaluate side-chains
  91 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   60 ILE
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  243 ASP
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 1 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    9.9990
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   chunk 45 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.8186

-------------------------------------------------------------------------------
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 = 0.116829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.091692 restraints weight = 7792.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.096607 restraints weight = 3520.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.099829 restraints weight = 2079.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5063  Z= 0.173
  Angle     :  0.496   5.568   6857  Z= 0.259
  Chirality :  0.041   0.192    744
  Planarity :  0.003   0.031    880
  Dihedral  :  3.881  13.824    674
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 11.09 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.34), residues: 608
  helix:  2.18 (0.34), residues: 265
  sheet: -1.15 (0.51), residues: 87
  loop :  0.75 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 122 
 HIS   0.004   0.001   HIS B  68 
 PHE   0.013   0.002   PHE A 159 
 TYR   0.015   0.001   TYR A 244 
 ARG   0.004   0.000   ARG B  52 

*********************** 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
  101 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8836 (mmt-90) cc_final: 0.8197 (mpt180)
REVERT: B   80 GLU cc_start: 0.8407 (tt0) cc_final: 0.8007 (tt0)
REVERT: B  101 PHE cc_start: 0.8768 (m-80) cc_final: 0.8527 (m-80)
REVERT: B  111 LEU cc_start: 0.8446 (tt) cc_final: 0.8135 (tt)
REVERT: A  147 ARG cc_start: 0.8710 (mmm160) cc_final: 0.8304 (mmm160)
REVERT: A  183 TYR cc_start: 0.8047 (m-80) cc_final: 0.7830 (m-80)
REVERT: A  243 ASP cc_start: 0.8836 (t0) cc_final: 0.8575 (t0)
REVERT: A  320 GLU cc_start: 0.8205 (tt0) cc_final: 0.7799 (tt0)
REVERT: A  340 LYS cc_start: 0.8817 (tttt) cc_final: 0.8526 (tptm)
REVERT: A  352 MET cc_start: 0.8976 (mtp) cc_final: 0.8462 (ttp)
REVERT: A  397 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8461 (pt0)
REVERT: A  427 TRP cc_start: 0.8026 (m100) cc_final: 0.7712 (m100)
  outliers start: 15
  outliers final: 10
  residues processed: 95
  average time/residue: 0.1620
  time to fit residues: 20.3877
Evaluate side-chains
  97 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
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  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  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 58 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0370
   chunk 48 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   overall best weight:    0.6660

-------------------------------------------------------------------------------
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 = 0.3581 r_free = 0.3581 target = 0.118763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.093245 restraints weight = 7715.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.098105 restraints weight = 3533.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.101401 restraints weight = 2107.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.4477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5063  Z= 0.158
  Angle     :  0.482   4.906   6857  Z= 0.253
  Chirality :  0.041   0.187    744
  Planarity :  0.003   0.031    880
  Dihedral  :  3.800  13.808    674
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.22 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.34), residues: 608
  helix:  2.19 (0.34), residues: 266
  sheet: -1.31 (0.50), residues: 87
  loop :  0.70 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 122 
 HIS   0.002   0.001   HIS B  68 
 PHE   0.011   0.001   PHE A 159 
 TYR   0.013   0.001   TYR B  86 
 ARG   0.008   0.000   ARG B  89 

*********************** 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
  104 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8341 (ttt-90) cc_final: 0.7442 (ttt90)
REVERT: B   52 ARG cc_start: 0.8873 (mmt-90) cc_final: 0.8459 (mpt180)
REVERT: B   80 GLU cc_start: 0.8711 (tt0) cc_final: 0.8053 (tt0)
REVERT: B   86 TYR cc_start: 0.8675 (m-80) cc_final: 0.8115 (m-10)
REVERT: B  101 PHE cc_start: 0.8831 (m-80) cc_final: 0.8624 (m-80)
REVERT: B  111 LEU cc_start: 0.8431 (tt) cc_final: 0.8059 (tt)
REVERT: A   48 GLU cc_start: 0.8633 (pp20) cc_final: 0.8371 (pp20)
REVERT: A  147 ARG cc_start: 0.8616 (mmm160) cc_final: 0.8300 (mmm160)
REVERT: A  243 ASP cc_start: 0.8811 (t0) cc_final: 0.8549 (t0)
REVERT: A  320 GLU cc_start: 0.8236 (tt0) cc_final: 0.7847 (tt0)
REVERT: A  340 LYS cc_start: 0.8826 (tttt) cc_final: 0.8534 (tptm)
REVERT: A  352 MET cc_start: 0.9036 (mtp) cc_final: 0.8762 (mtp)
  outliers start: 13
  outliers final: 12
  residues processed: 99
  average time/residue: 0.1770
  time to fit residues: 23.7713
Evaluate side-chains
  96 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 SER
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   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  339 ILE
Chi-restraints excluded: chain A residue  344 SER
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 18 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
B  54 GLN
A 160 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.102916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.078237 restraints weight = 8169.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.082499 restraints weight = 3869.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.085395 restraints weight = 2372.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.4627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   5063  Z= 0.414
  Angle     :  0.630   7.502   6857  Z= 0.332
  Chirality :  0.046   0.228    744
  Planarity :  0.004   0.034    880
  Dihedral  :  4.499  22.223    674
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 12.97 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.34), residues: 608
  helix:  1.79 (0.33), residues: 265
  sheet: -1.42 (0.53), residues: 87
  loop :  0.39 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 122 
 HIS   0.009   0.002   HIS B  68 
 PHE   0.014   0.002   PHE A 159 
 TYR   0.036   0.002   TYR A 489 
 ARG   0.004   0.001   ARG A 468 

*********************** 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
  97 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8354 (ttt-90) cc_final: 0.7425 (ttm-80)
REVERT: B   52 ARG cc_start: 0.8912 (mmt-90) cc_final: 0.8254 (mpt180)
REVERT: B   80 GLU cc_start: 0.8740 (tt0) cc_final: 0.8375 (tt0)
REVERT: B  101 PHE cc_start: 0.8801 (m-80) cc_final: 0.8513 (m-80)
REVERT: A  147 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8407 (mmm160)
REVERT: A  320 GLU cc_start: 0.8330 (tt0) cc_final: 0.7957 (tt0)
REVERT: A  340 LYS cc_start: 0.8798 (tttt) cc_final: 0.8480 (tptm)
REVERT: A  352 MET cc_start: 0.9152 (mtp) cc_final: 0.8602 (mtp)
REVERT: A  397 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8620 (pt0)
REVERT: A  489 TYR cc_start: 0.8653 (m-80) cc_final: 0.8419 (m-10)
  outliers start: 17
  outliers final: 14
  residues processed: 94
  average time/residue: 0.1759
  time to fit residues: 21.3018
Evaluate side-chains
  89 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
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  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  408 ILE
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 44 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3426 r_free = 0.3426 target = 0.108149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.083227 restraints weight = 7870.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.087712 restraints weight = 3646.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.090748 restraints weight = 2197.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.4831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5063  Z= 0.193
  Angle     :  0.516   5.799   6857  Z= 0.272
  Chirality :  0.042   0.175    744
  Planarity :  0.003   0.031    880
  Dihedral  :  4.061  15.852    674
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.35), residues: 608
  helix:  2.09 (0.34), residues: 265
  sheet: -1.78 (0.52), residues: 85
  loop :  0.43 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 122 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.010   0.001   PHE A 303 
 TYR   0.013   0.001   TYR A 489 
 ARG   0.002   0.000   ARG B  35 

*********************** 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
  94 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8385 (ttt-90) cc_final: 0.8032 (ttt90)
REVERT: B   52 ARG cc_start: 0.8928 (mmt-90) cc_final: 0.8491 (mpt180)
REVERT: B   80 GLU cc_start: 0.8669 (tt0) cc_final: 0.8359 (tt0)
REVERT: B  111 LEU cc_start: 0.8493 (tt) cc_final: 0.8148 (tt)
REVERT: A   24 GLU cc_start: 0.7694 (mp0) cc_final: 0.7456 (tp30)
REVERT: A   98 MET cc_start: 0.8625 (mmm) cc_final: 0.8132 (mmm)
REVERT: A  147 ARG cc_start: 0.8662 (mmm160) cc_final: 0.8351 (mmm160)
REVERT: A  207 PHE cc_start: 0.7906 (m-80) cc_final: 0.7567 (m-10)
REVERT: A  320 GLU cc_start: 0.8327 (tt0) cc_final: 0.7956 (tt0)
REVERT: A  340 LYS cc_start: 0.8801 (tttt) cc_final: 0.8508 (tptm)
REVERT: A  397 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8638 (pt0)
REVERT: A  400 LEU cc_start: 0.7791 (mm) cc_final: 0.7300 (pp)
  outliers start: 12
  outliers final: 11
  residues processed: 90
  average time/residue: 0.1601
  time to fit residues: 19.1207
Evaluate side-chains
  91 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
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   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  339 ILE
Chi-restraints excluded: chain A residue  344 SER
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 19 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 47 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 10 optimal weight:    0.3980
   chunk 9 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3386 r_free = 0.3386 target = 0.103994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.079360 restraints weight = 8183.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.083423 restraints weight = 3965.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.086207 restraints weight = 2461.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.5021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5063  Z= 0.204
  Angle     :  0.539   9.753   6857  Z= 0.279
  Chirality :  0.042   0.180    744
  Planarity :  0.003   0.030    880
  Dihedral  :  3.996  16.446    674
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.66 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.35), residues: 608
  helix:  2.05 (0.34), residues: 266
  sheet: -1.58 (0.53), residues: 83
  loop :  0.25 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 420 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.015   0.001   PHE B 101 
 TYR   0.013   0.001   TYR A 489 
 ARG   0.002   0.000   ARG A 490 

*********************** 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
  101 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8428 (ttt-90) cc_final: 0.7499 (ttm-80)
REVERT: B   52 ARG cc_start: 0.8904 (mmt-90) cc_final: 0.8547 (mpt180)
REVERT: B   80 GLU cc_start: 0.8691 (tt0) cc_final: 0.8308 (tt0)
REVERT: B  111 LEU cc_start: 0.8611 (tt) cc_final: 0.8314 (tt)
REVERT: A   49 GLU cc_start: 0.8193 (tp30) cc_final: 0.7971 (tp30)
REVERT: A  147 ARG cc_start: 0.8590 (mmm160) cc_final: 0.8277 (mmm160)
REVERT: A  207 PHE cc_start: 0.7978 (m-80) cc_final: 0.7603 (m-10)
REVERT: A  276 MET cc_start: 0.7374 (mmt) cc_final: 0.6963 (mmm)
REVERT: A  320 GLU cc_start: 0.8357 (tt0) cc_final: 0.7998 (tt0)
REVERT: A  340 LYS cc_start: 0.8853 (tttt) cc_final: 0.8586 (tptm)
REVERT: A  352 MET cc_start: 0.9014 (mtp) cc_final: 0.8441 (ttp)
REVERT: A  397 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8660 (pt0)
REVERT: A  400 LEU cc_start: 0.7905 (mm) cc_final: 0.7342 (pp)
REVERT: A  489 TYR cc_start: 0.8614 (m-10) cc_final: 0.8343 (m-10)
  outliers start: 13
  outliers final: 13
  residues processed: 96
  average time/residue: 0.1594
  time to fit residues: 20.3046
Evaluate side-chains
  94 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
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  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  339 ILE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  390 MET
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 51 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 44 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 492 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.104035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.079578 restraints weight = 8052.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.083577 restraints weight = 3912.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.086344 restraints weight = 2433.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.5134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5063  Z= 0.208
  Angle     :  0.561   9.101   6857  Z= 0.288
  Chirality :  0.042   0.155    744
  Planarity :  0.003   0.030    880
  Dihedral  :  3.972  16.406    674
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.66 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.35), residues: 608
  helix:  2.06 (0.34), residues: 265
  sheet: -1.65 (0.53), residues: 83
  loop :  0.32 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 420 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.014   0.001   PHE B 101 
 TYR   0.012   0.001   TYR A 188 
 ARG   0.002   0.000   ARG B  89 

*********************** 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
  101 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8436 (ttt-90) cc_final: 0.7498 (ttm-80)
REVERT: B   52 ARG cc_start: 0.8958 (mmt-90) cc_final: 0.8546 (mpt180)
REVERT: B   80 GLU cc_start: 0.8692 (tt0) cc_final: 0.8326 (tt0)
REVERT: B  111 LEU cc_start: 0.8609 (tt) cc_final: 0.8259 (tt)
REVERT: A  147 ARG cc_start: 0.8581 (mmm160) cc_final: 0.8276 (mmm160)
REVERT: A  207 PHE cc_start: 0.7981 (m-80) cc_final: 0.7538 (m-10)
REVERT: A  276 MET cc_start: 0.7349 (mmt) cc_final: 0.6903 (mmm)
REVERT: A  320 GLU cc_start: 0.8360 (tt0) cc_final: 0.8018 (tt0)
REVERT: A  340 LYS cc_start: 0.8857 (tttt) cc_final: 0.8594 (tptm)
REVERT: A  352 MET cc_start: 0.9016 (mtp) cc_final: 0.8778 (ttm)
REVERT: A  397 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8673 (pt0)
REVERT: A  489 TYR cc_start: 0.8527 (m-10) cc_final: 0.8297 (m-10)
  outliers start: 17
  outliers final: 13
  residues processed: 95
  average time/residue: 0.1655
  time to fit residues: 20.7747
Evaluate side-chains
  93 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
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   51 VAL
Chi-restraints excluded: chain A residue   60 ILE
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  339 ILE
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  390 MET
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 51 optimal weight:    7.9990
   chunk 6 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 27 optimal weight:    0.4980
   chunk 49 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 455 HIS
A 492 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.106080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.081677 restraints weight = 8081.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.085816 restraints weight = 3890.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.088655 restraints weight = 2391.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.5265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5063  Z= 0.178
  Angle     :  0.557   9.152   6857  Z= 0.282
  Chirality :  0.042   0.197    744
  Planarity :  0.003   0.030    880
  Dihedral  :  3.833  15.957    674
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 15.79 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.35), residues: 608
  helix:  2.16 (0.34), residues: 265
  sheet: -1.69 (0.52), residues: 83
  loop :  0.32 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 427 
 HIS   0.002   0.001   HIS A 455 
 PHE   0.015   0.001   PHE B 101 
 TYR   0.012   0.001   TYR A 188 
 ARG   0.002   0.000   ARG B  89 

********************** 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: 12
    poor density    : 84
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8417 (ttt-90) cc_final: 0.7586 (ttm-80)
REVERT: B   52 ARG cc_start: 0.8938 (mmt-90) cc_final: 0.8516 (mmp80)
REVERT: B   80 GLU cc_start: 0.8639 (tt0) cc_final: 0.8285 (tt0)
REVERT: B  111 LEU cc_start: 0.8600 (tt) cc_final: 0.8238 (tt)
REVERT: A   24 GLU cc_start: 0.7237 (pm20) cc_final: 0.6782 (tp30)
REVERT: A  147 ARG cc_start: 0.8630 (mmm160) cc_final: 0.8302 (mmm160)
REVERT: A  320 GLU cc_start: 0.8337 (tt0) cc_final: 0.7976 (tt0)
REVERT: A  340 LYS cc_start: 0.8844 (tttt) cc_final: 0.8572 (tptm)
REVERT: A  397 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8647 (pt0)
  outliers start: 12
  outliers final: 12
  residues processed: 90
  average time/residue: 0.1625
  time to fit residues: 19.0476
Evaluate side-chains
  94 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
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   51 VAL
Chi-restraints excluded: chain A residue   60 ILE
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  339 ILE
Chi-restraints excluded: chain A residue  390 MET
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 24 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   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  11 ASN
A 455 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.105326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.081093 restraints weight = 8081.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.085176 restraints weight = 3879.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.088019 restraints weight = 2391.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.5290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5063  Z= 0.203
  Angle     :  0.579   9.243   6857  Z= 0.295
  Chirality :  0.042   0.160    744
  Planarity :  0.003   0.030    880
  Dihedral  :  3.820  15.700    674
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.60 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.35), residues: 608
  helix:  2.18 (0.34), residues: 264
  sheet: -1.77 (0.53), residues: 83
  loop :  0.29 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 420 
 HIS   0.004   0.001   HIS A 455 
 PHE   0.014   0.001   PHE B 101 
 TYR   0.019   0.001   TYR A 488 
 ARG   0.002   0.000   ARG B  89 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1857.58 seconds
wall clock time: 34 minutes 33.56 seconds (2073.56 seconds total)