Starting phenix.real_space_refine
on Thu Jul 24 02:26:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lms_23441/07_2025/7lms_23441.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lms_23441/07_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_23441/07_2025/7lms_23441.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lms_23441/07_2025/7lms_23441.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lms_23441/07_2025/7lms_23441.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lms_23441/07_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 3.65, per 1000 atoms: 0.74
  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: 1.91
  Conformation dependent library (CDL) restraints added in 676.9 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: 0.60
  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: 1.44

  Time building geometry restraints manager: 1.51 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:             8.150
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     17.600
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.190
-------------------------------------------------------------------------------
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 (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 

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

*********************** 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  : 0.702 
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: 0.2080
  time to fit residues: 41.0521
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  : 0.877 
-------------------------------------------------------------------------------
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 = 28)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.096039 restraints weight = 7417.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.101006 restraints weight = 3330.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.104287 restraints weight = 1950.360|
|-----------------------------------------------------------------------------|
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   5067  Z= 0.138
  Angle     :  0.590   7.672   6860  Z= 0.310
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05388 (  236)
  hydrogen bonds       : angle       4.26629 (  663)
  metal coordination   : bond        0.01270 (    4)
  metal coordination   : angle       5.92300 (    3)
  covalent geometry    : bond        0.00299 ( 5063)
  covalent geometry    : angle       0.57699 ( 6857)

*********************** 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  : 0.516 
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: 0.8270 (mtp)
REVERT: A  397 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8566 (mm-30)
REVERT: A  423 GLU cc_start: 0.7731 (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: 0.1687
  time to fit residues: 23.4322
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  : 0.752 
-------------------------------------------------------------------------------
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:    0.2980
   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:    0.9980
   chunk 28 optimal weight:    0.0170
   chunk 30 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.5820

-------------------------------------------------------------------------------
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 = 0.3503 r_free = 0.3503 target = 0.113034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.088371 restraints weight = 7741.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.093239 restraints weight = 3466.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.096546 restraints weight = 2023.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5067  Z= 0.111
  Angle     :  0.525   6.625   6860  Z= 0.273
  Chirality :  0.042   0.197    744
  Planarity :  0.003   0.034    880
  Dihedral  :  4.028  13.961    674
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  :  9.02 %
    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 (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 (0.34), residues: 259
  sheet: -0.96 (0.53), residues: 85
  loop :  0.92 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 122 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.015   0.002   PHE A 159 
 TYR   0.025   0.002   TYR B  86 
 ARG   0.004   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04123 (  236)
  hydrogen bonds       : angle       3.77911 (  663)
  metal coordination   : bond        0.01156 (    4)
  metal coordination   : angle       4.67815 (    3)
  covalent geometry    : bond        0.00239 ( 5063)
  covalent geometry    : angle       0.51549 ( 6857)

*********************** 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
  112 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 2.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8338 (ttt-90) cc_final: 0.7359 (ttm170)
REVERT: B   52 ARG cc_start: 0.8701 (mmt-90) cc_final: 0.7942 (mpt180)
REVERT: B   91 TYR cc_start: 0.7660 (m-80) cc_final: 0.7447 (m-80)
REVERT: B  101 PHE cc_start: 0.8751 (m-80) cc_final: 0.8476 (m-80)
REVERT: B  111 LEU cc_start: 0.8397 (tt) cc_final: 0.8131 (tt)
REVERT: B  114 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8319 (mp0)
REVERT: A  183 TYR cc_start: 0.8055 (m-80) cc_final: 0.7820 (m-80)
REVERT: A  320 GLU cc_start: 0.8153 (tt0) cc_final: 0.7734 (tt0)
REVERT: A  340 LYS cc_start: 0.8774 (tttt) cc_final: 0.8493 (tptm)
REVERT: A  352 MET cc_start: 0.8975 (mtp) cc_final: 0.8611 (mtp)
REVERT: A  427 TRP cc_start: 0.7893 (m100) cc_final: 0.7594 (m100)
  outliers start: 15
  outliers final: 10
  residues processed: 103
  average time/residue: 0.2842
  time to fit residues: 40.0339
Evaluate side-chains
  96 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
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   60 ILE
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  266 VAL
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:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 20 optimal weight:    0.4980
   chunk 9 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0040
   chunk 53 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.6394

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.118296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.093230 restraints weight = 7740.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.098189 restraints weight = 3496.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.101462 restraints weight = 2056.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5067  Z= 0.108
  Angle     :  0.494   6.240   6860  Z= 0.256
  Chirality :  0.041   0.194    744
  Planarity :  0.004   0.046    880
  Dihedral  :  3.839  13.916    674
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 11.09 %
    Favored  : 86.47 %
  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:  1.55 (0.34), residues: 608
  helix:  2.21 (0.34), residues: 266
  sheet: -1.20 (0.51), residues: 87
  loop :  0.76 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 122 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.012   0.001   PHE A 159 
 TYR   0.015   0.001   TYR A 244 
 ARG   0.009   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03815 (  236)
  hydrogen bonds       : angle       3.61863 (  663)
  metal coordination   : bond        0.01161 (    4)
  metal coordination   : angle       3.99976 (    3)
  covalent geometry    : bond        0.00239 ( 5063)
  covalent geometry    : angle       0.48714 ( 6857)

*********************** 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: 13
    poor density    : 88
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8820 (mmt-90) cc_final: 0.8580 (mpt180)
REVERT: B  101 PHE cc_start: 0.8786 (m-80) cc_final: 0.8532 (m-80)
REVERT: B  111 LEU cc_start: 0.8396 (tt) cc_final: 0.8027 (tt)
REVERT: A   48 GLU cc_start: 0.8629 (pp20) cc_final: 0.8391 (pp20)
REVERT: A  147 ARG cc_start: 0.8706 (mmm160) cc_final: 0.8306 (mmm160)
REVERT: A  183 TYR cc_start: 0.8051 (m-80) cc_final: 0.7791 (m-80)
REVERT: A  243 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8538 (t0)
REVERT: A  320 GLU cc_start: 0.8174 (tt0) cc_final: 0.7758 (tt0)
REVERT: A  340 LYS cc_start: 0.8789 (tttt) cc_final: 0.8505 (tptm)
REVERT: A  352 MET cc_start: 0.8949 (mtp) cc_final: 0.8435 (mtp)
REVERT: A  397 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8422 (pt0)
  outliers start: 13
  outliers final: 8
  residues processed: 94
  average time/residue: 0.2607
  time to fit residues: 33.1411
Evaluate side-chains
  96 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 1.953 
-------------------------------------------------------------------------------
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  243 ASP
Chi-restraints excluded: chain A residue  339 ILE
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:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 49 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0970
   chunk 48 optimal weight:    0.1980
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.3778

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.120385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.095452 restraints weight = 7624.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.100449 restraints weight = 3441.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.103726 restraints weight = 2014.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.4565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5067  Z= 0.091
  Angle     :  0.466   4.896   6860  Z= 0.242
  Chirality :  0.040   0.182    744
  Planarity :  0.003   0.031    880
  Dihedral  :  3.659  13.704    674
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.59 %
    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 (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:  1.55 (0.34), residues: 608
  helix:  2.26 (0.34), residues: 264
  sheet: -1.32 (0.50), residues: 87
  loop :  0.75 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 122 
 HIS   0.002   0.000   HIS B  45 
 PHE   0.010   0.001   PHE A 159 
 TYR   0.026   0.001   TYR A 489 
 ARG   0.007   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03333 (  236)
  hydrogen bonds       : angle       3.45082 (  663)
  metal coordination   : bond        0.00941 (    4)
  metal coordination   : angle       3.42470 (    3)
  covalent geometry    : bond        0.00192 ( 5063)
  covalent geometry    : angle       0.46031 ( 6857)

*********************** 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  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8905 (mmt-90) cc_final: 0.8418 (mpt180)
REVERT: B   80 GLU cc_start: 0.8736 (tt0) cc_final: 0.7982 (tt0)
REVERT: B   86 TYR cc_start: 0.8638 (m-80) cc_final: 0.8090 (m-10)
REVERT: B   89 ARG cc_start: 0.8623 (ttt-90) cc_final: 0.8303 (ttt-90)
REVERT: B  101 PHE cc_start: 0.8828 (m-80) cc_final: 0.8615 (m-80)
REVERT: B  111 LEU cc_start: 0.8418 (tt) cc_final: 0.8063 (tt)
REVERT: A  147 ARG cc_start: 0.8620 (mmm160) cc_final: 0.8309 (mmm160)
REVERT: A  320 GLU cc_start: 0.8184 (tt0) cc_final: 0.7778 (tt0)
REVERT: A  340 LYS cc_start: 0.8813 (tttt) cc_final: 0.8527 (tptm)
REVERT: A  352 MET cc_start: 0.9000 (mtp) cc_final: 0.8725 (mtp)
REVERT: A  397 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8438 (pt0)
  outliers start: 13
  outliers final: 11
  residues processed: 100
  average time/residue: 0.2238
  time to fit residues: 29.7299
Evaluate side-chains
  93 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
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  224 ILE
Chi-restraints excluded: chain A residue  266 VAL
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:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  54 GLN
B  92 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.103356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.078531 restraints weight = 8162.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.082794 restraints weight = 3871.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.085684 restraints weight = 2373.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.4618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067   5067  Z= 0.277
  Angle     :  0.660  10.146   6860  Z= 0.342
  Chirality :  0.046   0.215    744
  Planarity :  0.004   0.034    880
  Dihedral  :  4.438  21.294    674
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.72 %
    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 (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:  1.07 (0.34), residues: 608
  helix:  1.77 (0.33), residues: 265
  sheet: -1.32 (0.53), residues: 87
  loop :  0.49 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 122 
 HIS   0.008   0.002   HIS B  68 
 PHE   0.013   0.002   PHE A 303 
 TYR   0.021   0.002   TYR A 241 
 ARG   0.005   0.001   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05382 (  236)
  hydrogen bonds       : angle       4.32317 (  663)
  metal coordination   : bond        0.01838 (    4)
  metal coordination   : angle       5.97479 (    3)
  covalent geometry    : bond        0.00656 ( 5063)
  covalent geometry    : angle       0.64833 ( 6857)

*********************** 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
  98 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8346 (ttt-90) cc_final: 0.7856 (ttt180)
REVERT: B   26 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8932 (mm110)
REVERT: B   52 ARG cc_start: 0.8992 (mmt-90) cc_final: 0.8508 (mpt180)
REVERT: B   80 GLU cc_start: 0.8613 (tt0) cc_final: 0.8395 (tt0)
REVERT: B  101 PHE cc_start: 0.8805 (m-80) cc_final: 0.8535 (m-80)
REVERT: A  147 ARG cc_start: 0.8677 (mmm160) cc_final: 0.8400 (mmm160)
REVERT: A  183 TYR cc_start: 0.8065 (m-80) cc_final: 0.7861 (m-80)
REVERT: A  320 GLU cc_start: 0.8312 (tt0) cc_final: 0.7931 (tt0)
REVERT: A  340 LYS cc_start: 0.8795 (tttt) cc_final: 0.8474 (tptm)
REVERT: A  352 MET cc_start: 0.9132 (mtp) cc_final: 0.8922 (ttm)
REVERT: A  397 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8520 (pt0)
  outliers start: 17
  outliers final: 15
  residues processed: 94
  average time/residue: 0.2842
  time to fit residues: 35.1879
Evaluate side-chains
  88 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
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   57 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  415 GLU
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:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.108808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.083924 restraints weight = 7895.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.088443 restraints weight = 3656.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.091512 restraints weight = 2196.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.4851

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= 0.121
  Angle     :  0.534   8.318   6860  Z= 0.275
  Chirality :  0.042   0.179    744
  Planarity :  0.003   0.034    880
  Dihedral  :  4.006  14.610    674
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 15.04 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.20 (0.35), residues: 608
  helix:  2.06 (0.34), residues: 266
  sheet: -1.74 (0.51), residues: 85
  loop :  0.52 (0.37), residues: 257

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   0.009   0.001   PHE A 303 
 TYR   0.016   0.001   TYR A 489 
 ARG   0.006   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04030 (  236)
  hydrogen bonds       : angle       3.71406 (  663)
  metal coordination   : bond        0.01150 (    4)
  metal coordination   : angle       5.06094 (    3)
  covalent geometry    : bond        0.00279 ( 5063)
  covalent geometry    : angle       0.52322 ( 6857)

*********************** 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
  98 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 2.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8415 (ttt-90) cc_final: 0.7479 (ttm-80)
REVERT: B   52 ARG cc_start: 0.8958 (mmt-90) cc_final: 0.8486 (mpt180)
REVERT: B   80 GLU cc_start: 0.8769 (tt0) cc_final: 0.8034 (tt0)
REVERT: B   89 ARG cc_start: 0.8612 (ttt-90) cc_final: 0.8233 (ttt-90)
REVERT: B  111 LEU cc_start: 0.8533 (tt) cc_final: 0.8184 (tt)
REVERT: A   24 GLU cc_start: 0.7668 (mp0) cc_final: 0.7463 (tp30)
REVERT: A  147 ARG cc_start: 0.8634 (mmm160) cc_final: 0.8329 (mmm160)
REVERT: A  320 GLU cc_start: 0.8314 (tt0) cc_final: 0.7937 (tt0)
REVERT: A  340 LYS cc_start: 0.8804 (tttt) cc_final: 0.8521 (tptm)
REVERT: A  352 MET cc_start: 0.9067 (mtp) cc_final: 0.8858 (ttm)
REVERT: A  397 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8491 (pt0)
REVERT: A  400 LEU cc_start: 0.7836 (mm) cc_final: 0.7304 (pp)
  outliers start: 12
  outliers final: 12
  residues processed: 94
  average time/residue: 0.1927
  time to fit residues: 25.2667
Evaluate side-chains
  92 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
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  224 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  344 SER
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 19 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.106010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.081079 restraints weight = 8167.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.085517 restraints weight = 3786.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.088521 restraints weight = 2290.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.4932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5067  Z= 0.183
  Angle     :  0.584   8.986   6860  Z= 0.302
  Chirality :  0.044   0.236    744
  Planarity :  0.004   0.034    880
  Dihedral  :  4.154  16.413    674
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.85 %
    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:  1.10 (0.35), residues: 608
  helix:  1.97 (0.34), residues: 265
  sheet: -1.65 (0.53), residues: 81
  loop :  0.38 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 122 
 HIS   0.005   0.001   HIS B  68 
 PHE   0.014   0.002   PHE B 101 
 TYR   0.013   0.002   TYR A 241 
 ARG   0.007   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04507 (  236)
  hydrogen bonds       : angle       3.93345 (  663)
  metal coordination   : bond        0.01449 (    4)
  metal coordination   : angle       5.34370 (    3)
  covalent geometry    : bond        0.00434 ( 5063)
  covalent geometry    : angle       0.57369 ( 6857)

*********************** 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
  97 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8417 (ttt-90) cc_final: 0.7451 (ttm-80)
REVERT: B   52 ARG cc_start: 0.8988 (mmt-90) cc_final: 0.8497 (mpt180)
REVERT: B   80 GLU cc_start: 0.8725 (tt0) cc_final: 0.8292 (tt0)
REVERT: B  111 LEU cc_start: 0.8533 (tt) cc_final: 0.8249 (tt)
REVERT: A   24 GLU cc_start: 0.7700 (mp0) cc_final: 0.7464 (tp30)
REVERT: A  147 ARG cc_start: 0.8664 (mmm160) cc_final: 0.8332 (mmm160)
REVERT: A  207 PHE cc_start: 0.7949 (m-10) cc_final: 0.7638 (m-10)
REVERT: A  320 GLU cc_start: 0.8346 (tt0) cc_final: 0.7956 (tt0)
REVERT: A  340 LYS cc_start: 0.8825 (tttt) cc_final: 0.8538 (tptm)
REVERT: A  352 MET cc_start: 0.9086 (mtp) cc_final: 0.8869 (ttm)
REVERT: A  397 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8513 (pt0)
  outliers start: 16
  outliers final: 16
  residues processed: 91
  average time/residue: 0.2182
  time to fit residues: 26.4555
Evaluate side-chains
  94 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
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   57 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  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 51 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 43 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B  11 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.107971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.083354 restraints weight = 7985.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.087749 restraints weight = 3773.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.090691 restraints weight = 2295.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.5091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5067  Z= 0.138
  Angle     :  0.554   8.865   6860  Z= 0.282
  Chirality :  0.043   0.215    744
  Planarity :  0.003   0.032    880
  Dihedral  :  4.047  16.734    674
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.23 %
    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:  1.10 (0.35), residues: 608
  helix:  2.08 (0.34), residues: 265
  sheet: -1.71 (0.53), residues: 81
  loop :  0.26 (0.36), residues: 262

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   0.014   0.001   PHE B 101 
 TYR   0.012   0.001   TYR A 489 
 ARG   0.003   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03981 (  236)
  hydrogen bonds       : angle       3.74081 (  663)
  metal coordination   : bond        0.01249 (    4)
  metal coordination   : angle       4.81990 (    3)
  covalent geometry    : bond        0.00322 ( 5063)
  covalent geometry    : angle       0.54485 ( 6857)

*********************** 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
  95 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8398 (ttt-90) cc_final: 0.7502 (ttm-80)
REVERT: B   52 ARG cc_start: 0.8981 (mmt-90) cc_final: 0.8459 (mpt180)
REVERT: B  111 LEU cc_start: 0.8469 (tt) cc_final: 0.8112 (tt)
REVERT: A   24 GLU cc_start: 0.7733 (mp0) cc_final: 0.7483 (tp30)
REVERT: A  147 ARG cc_start: 0.8688 (mmm160) cc_final: 0.8352 (mmm160)
REVERT: A  207 PHE cc_start: 0.7925 (m-10) cc_final: 0.7646 (m-10)
REVERT: A  320 GLU cc_start: 0.8305 (tt0) cc_final: 0.7923 (tt0)
REVERT: A  340 LYS cc_start: 0.8794 (tttt) cc_final: 0.8514 (tptm)
REVERT: A  352 MET cc_start: 0.9114 (mtp) cc_final: 0.8901 (ttm)
REVERT: A  397 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8469 (pt0)
REVERT: A  489 TYR cc_start: 0.8237 (m-10) cc_final: 0.7956 (m-10)
  outliers start: 15
  outliers final: 13
  residues processed: 88
  average time/residue: 0.2941
  time to fit residues: 35.8725
Evaluate side-chains
  89 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
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  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  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 51 optimal weight:    0.0370
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0570
   chunk 26 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.4576

-------------------------------------------------------------------------------
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
A 492 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.111044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.086103 restraints weight = 7906.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.090675 restraints weight = 3618.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.093801 restraints weight = 2159.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.5243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5067  Z= 0.108
  Angle     :  0.552   9.449   6860  Z= 0.280
  Chirality :  0.043   0.219    744
  Planarity :  0.003   0.031    880
  Dihedral  :  3.880  16.177    674
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.35 %
    Favored  : 81.20 %
  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:  1.29 (0.35), residues: 608
  helix:  2.44 (0.34), residues: 258
  sheet: -1.88 (0.51), residues: 87
  loop :  0.34 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 420 
 HIS   0.004   0.001   HIS A 455 
 PHE   0.015   0.001   PHE B 101 
 TYR   0.010   0.001   TYR A 188 
 ARG   0.002   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03653 (  236)
  hydrogen bonds       : angle       3.68593 (  663)
  metal coordination   : bond        0.00960 (    4)
  metal coordination   : angle       4.04670 (    3)
  covalent geometry    : bond        0.00240 ( 5063)
  covalent geometry    : angle       0.54549 ( 6857)

********************** 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
  92 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 ARG cc_start: 0.8407 (ttt-90) cc_final: 0.7557 (ttm-80)
REVERT: B   52 ARG cc_start: 0.8947 (mmt-90) cc_final: 0.8541 (mpt180)
REVERT: B   80 GLU cc_start: 0.8627 (tt0) cc_final: 0.8217 (tt0)
REVERT: B  111 LEU cc_start: 0.8544 (tt) cc_final: 0.8164 (tt)
REVERT: A  147 ARG cc_start: 0.8659 (mmm160) cc_final: 0.8325 (mmm160)
REVERT: A  320 GLU cc_start: 0.8302 (tt0) cc_final: 0.7943 (tt0)
REVERT: A  340 LYS cc_start: 0.8823 (tttt) cc_final: 0.8545 (tptm)
REVERT: A  397 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8477 (pt0)
  outliers start: 13
  outliers final: 11
  residues processed: 88
  average time/residue: 0.2155
  time to fit residues: 25.6424
Evaluate side-chains
  89 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
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  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  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:    0.0370
   chunk 32 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.9060

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

Flipped N/Q/H residues before XYZ refinement:
B  11 ASN
B  92 GLN
A 455 HIS
A 492 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.105687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.081401 restraints weight = 8103.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.085506 restraints weight = 3891.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.088342 restraints weight = 2392.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.5335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5067  Z= 0.130
  Angle     :  0.574   9.294   6860  Z= 0.291
  Chirality :  0.043   0.213    744
  Planarity :  0.003   0.030    880
  Dihedral  :  3.918  16.302    674
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.92 %
    Favored  : 80.64 %
  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:  1.23 (0.35), residues: 608
  helix:  2.40 (0.34), residues: 259
  sheet: -1.84 (0.52), residues: 83
  loop :  0.22 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 420 
 HIS   0.004   0.001   HIS A 455 
 PHE   0.014   0.001   PHE B 101 
 TYR   0.010   0.001   TYR A 241 
 ARG   0.002   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03929 (  236)
  hydrogen bonds       : angle       3.77302 (  663)
  metal coordination   : bond        0.01156 (    4)
  metal coordination   : angle       4.36637 (    3)
  covalent geometry    : bond        0.00300 ( 5063)
  covalent geometry    : angle       0.56637 ( 6857)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3550.40 seconds
wall clock time: 68 minutes 5.37 seconds (4085.37 seconds total)