Starting phenix.real_space_refine
on Tue Mar 11 15:36:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9caj_45393/03_2025/9caj_45393_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9caj_45393/03_2025/9caj_45393.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9caj_45393/03_2025/9caj_45393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9caj_45393/03_2025/9caj_45393.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9caj_45393/03_2025/9caj_45393_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9caj_45393/03_2025/9caj_45393_neut.cif"
  }
  resolution = 3.51
  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=   0.020
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: 6
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     P       9      5.49       5
     S      39      5.16       5
     C    3918      2.51       5
     N    1079      2.21       5
     O    1199      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6245
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4840
          Classifications: {'peptide': 612}
          Link IDs: {'PTRANS': 30, 'TRANS': 581}
    Chain: "B"
      Number of atoms: 1219
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1219
          Classifications: {'peptide': 161}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 153}
    Chain: "C"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 185
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.94, per 1000 atoms: 0.79
  Number of scatterers: 6245
  At special positions: 0
  Unit cell: (76.36, 87.15, 138.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      1     24.99
     S      39     16.00
     P       9     15.00
     O    1199      8.00
     N    1079      7.00
     C    3918      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: 1.65
  Conformation dependent library (CDL) restraints added in 913.2 milliseconds
  

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1442

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      41.1% alpha, 14.9% beta
      0 base pairs and 4 stacking pairs defined.
    Time for finding SS restraints: 2.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 22
      removed outlier: 4.105A  pdb=" N   ILE A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 4.336A  pdb=" N   SER A  83 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 106
    Processing helix  chain 'A' and resid 119 through 134
    Processing helix  chain 'A' and resid 157 through 165
      removed outlier: 4.549A  pdb=" N   CYS A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 201
      removed outlier: 3.706A  pdb=" N   SER A 177 " --> pdb=" O   ASN A 173 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   VAL A 178 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASP A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   CYS A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ALA A 191 " --> pdb=" O   ARG A 187 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   PHE A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   THR A 193 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 208
      removed outlier: 3.563A  pdb=" N   LEU A 207 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 233
      removed outlier: 3.708A  pdb=" N   CYS A 225 " --> pdb=" O   THR A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 276
      removed outlier: 3.682A  pdb=" N   ALA A 270 " --> pdb=" O   ASP A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 313
    Processing helix  chain 'A' and resid 317 through 332
    Processing helix  chain 'A' and resid 349 through 357
      removed outlier: 3.714A  pdb=" N   GLN A 357 " --> pdb=" O   SER A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 374
    Processing helix  chain 'A' and resid 403 through 421
      removed outlier: 3.718A  pdb=" N   TYR A 411 " --> pdb=" O   ARG A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 455
    Processing helix  chain 'A' and resid 495 through 507
    Processing helix  chain 'A' and resid 513 through 524
    Processing helix  chain 'A' and resid 538 through 551
    Processing helix  chain 'A' and resid 552 through 556
      removed outlier: 3.899A  pdb=" N   VAL A 556 " --> pdb=" O   ALA A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 574
      removed outlier: 3.645A  pdb=" N   SER A 562 " --> pdb=" O   PRO A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 600
      removed outlier: 3.576A  pdb=" N   ASP A 598 " --> pdb=" O   HIS A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 609
      removed outlier: 3.967A  pdb=" N   VAL A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 13
    Processing helix  chain 'B' and resid 17 through 25
    Processing helix  chain 'B' and resid 32 through 43
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3
      removed outlier: 6.232A  pdb=" N   LYS A   2 " --> pdb=" O   ARG A  51 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   LYS A  53 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   TYR A  41 " --> pdb=" O   PHE A  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 3
      removed outlier: 6.232A  pdb=" N   LYS A   2 " --> pdb=" O   ARG A  51 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   LYS A  53 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   MET A   6 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   LEU A   5 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   TRP A 115 " --> pdb=" O   LEU A   5 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   VAL A   7 " --> pdb=" O   TRP A 115 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 66
    Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 244
    Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 247
    Processing sheet with id=AA6, first strand: chain 'A' and resid 258 through 259
      removed outlier: 6.939A  pdb=" N   LYS A 425 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   CYS A 424 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ALA A 294 " --> pdb=" O   CYS A 424 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   TYR A 426 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   GLU A 292 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   GLN A 428 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   ARG A 290 " --> pdb=" O   GLN A 428 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   THR A 430 " --> pdb=" O   THR A 288 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   THR A 288 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   SER A 432 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 530
    Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 65
      removed outlier: 4.646A  pdb=" N   ASP B 134 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 9.111A  pdb=" N   LEU B 140 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   THR B 107 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ARG B  96 " --> pdb=" O   ILE B  76 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   ILE B  76 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   GLN B  98 " --> pdb=" O   GLN B  74 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LYS B 126 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)

    258 hydrogen bonds defined for protein.
    732 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      4 stacking parallelities
  Total time for adding SS restraints: 1.98

  Time building geometry restraints manager: 1.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2011
        1.34 -     1.45: 886
        1.45 -     1.57: 3415
        1.57 -     1.69: 17
        1.69 -     1.81: 61
  Bond restraints: 6390
  Sorted by residual:
  bond pdb=" N   LYS A  10 "
       pdb=" CA  LYS A  10 "
    ideal  model  delta    sigma   weight residual
    1.453  1.480 -0.027 1.18e-02 7.18e+03 5.18e+00
  bond pdb=" N   ARG A 338 "
       pdb=" CA  ARG A 338 "
    ideal  model  delta    sigma   weight residual
    1.462  1.494 -0.032 1.46e-02 4.69e+03 4.75e+00
  bond pdb=" N   GLU A 340 "
       pdb=" CA  GLU A 340 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.61e-02 3.86e+03 3.77e+00
  bond pdb=" O3'  DA C  -1 "
       pdb=" P    DC C   0 "
    ideal  model  delta    sigma   weight residual
    1.607  1.579  0.028 1.50e-02 4.44e+03 3.56e+00
  bond pdb=" O3'  DT C   4 "
       pdb=" P    DA C   5 "
    ideal  model  delta    sigma   weight residual
    1.607  1.580  0.027 1.50e-02 4.44e+03 3.36e+00
  ... (remaining 6385 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 8420
        1.67 -     3.33: 205
        3.33 -     5.00: 44
        5.00 -     6.67: 11
        6.67 -     8.34: 3
  Bond angle restraints: 8683
  Sorted by residual:
  angle pdb=" C4'  DA C  -1 "
        pdb=" C3'  DA C  -1 "
        pdb=" O3'  DA C  -1 "
      ideal   model   delta    sigma   weight residual
     110.00  103.81    6.19 1.50e+00 4.44e-01 1.71e+01
  angle pdb=" C   LYS A  10 "
        pdb=" N   PRO A  11 "
        pdb=" CA  PRO A  11 "
      ideal   model   delta    sigma   weight residual
     119.84  124.02   -4.18 1.25e+00 6.40e-01 1.12e+01
  angle pdb=" C   CYS A 109 "
        pdb=" N   ASP A 110 "
        pdb=" CA  ASP A 110 "
      ideal   model   delta    sigma   weight residual
     121.54  127.52   -5.98 1.91e+00 2.74e-01 9.80e+00
  angle pdb=" N   GLY B  60 "
        pdb=" CA  GLY B  60 "
        pdb=" C   GLY B  60 "
      ideal   model   delta    sigma   weight residual
     114.25  118.20   -3.95 1.30e+00 5.92e-01 9.23e+00
  angle pdb=" O3'  DT C   4 "
        pdb=" C3'  DT C   4 "
        pdb=" C2'  DT C   4 "
      ideal   model   delta    sigma   weight residual
     111.50  107.00    4.50 1.50e+00 4.44e-01 9.00e+00
  ... (remaining 8678 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3408
       17.97 -    35.94: 345
       35.94 -    53.91: 76
       53.91 -    71.88: 24
       71.88 -    89.85: 9
  Dihedral angle restraints: 3862
    sinusoidal: 1628
      harmonic: 2234
  Sorted by residual:
  dihedral pdb=" CA  VAL A 113 "
           pdb=" C   VAL A 113 "
           pdb=" N   LEU A 114 "
           pdb=" CA  LEU A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.48  -21.52     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" CA  TYR A 111 "
           pdb=" C   TYR A 111 "
           pdb=" N   ILE A 112 "
           pdb=" CA  ILE A 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.04   20.96     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  ASP A 552 "
           pdb=" C   ASP A 552 "
           pdb=" N   ALA A 553 "
           pdb=" CA  ALA A 553 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.21  -17.79     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 3859 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 756
       0.047 -    0.093: 175
       0.093 -    0.139: 39
       0.139 -    0.186: 3
       0.186 -    0.232: 1
  Chirality restraints: 974
  Sorted by residual:
  chirality pdb=" CB  ILE A 435 "
            pdb=" CA  ILE A 435 "
            pdb=" CG1 ILE A 435 "
            pdb=" CG2 ILE A 435 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" C3'  DT C   4 "
            pdb=" C4'  DT C   4 "
            pdb=" O3'  DT C   4 "
            pdb=" C2'  DT C   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.82    0.16 2.00e-01 2.50e+01 6.10e-01
  chirality pdb=" CA  VAL A   4 "
            pdb=" N   VAL A   4 "
            pdb=" C   VAL A   4 "
            pdb=" CB  VAL A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.15 2.00e-01 2.50e+01 5.94e-01
  ... (remaining 971 not shown)

  Planarity restraints: 1091
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 436 "   -0.055 5.00e-02 4.00e+02   8.52e-02 1.16e+01
        pdb=" N   PRO A 437 "    0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO A 437 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 437 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 456 "   -0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO A 457 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 457 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 457 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  53 "   -0.027 5.00e-02 4.00e+02   4.17e-02 2.79e+00
        pdb=" N   PRO B  54 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B  54 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  54 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1088 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 83
        2.65 -     3.21: 5753
        3.21 -     3.78: 9333
        3.78 -     4.34: 12421
        4.34 -     4.90: 20680
  Nonbonded interactions: 48270
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   9 "
            pdb=" OD2 ASP A 117 "
     model   vdw
     2.088 3.040
  nonbonded pdb=" OE2 GLU A   9 "
            pdb="MN    MN A 701 "
     model   vdw
     2.124 2.320
  nonbonded pdb=" OP1  DA C   5 "
            pdb="MN    MN A 701 "
     model   vdw
     2.151 2.320
  nonbonded pdb=" OG  SER A 289 "
            pdb=" OG1 THR A 430 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OH  TYR A 204 "
            pdb=" OD1 ASP A 604 "
     model   vdw
     2.296 3.040
  ... (remaining 48265 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:             2.090
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     21.000
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   6390  Z= 0.237
  Angle     :  0.663   8.336   8683  Z= 0.360
  Chirality :  0.042   0.232    974
  Planarity :  0.005   0.085   1091
  Dihedral  : 15.919  89.853   2420
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  0.60 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.25 (0.31), residues: 769
  helix:  1.05 (0.30), residues: 293
  sheet: -0.50 (0.45), residues: 148
  loop : -1.07 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 458 
 HIS   0.007   0.001   HIS B 156 
 PHE   0.011   0.001   PHE B  52 
 TYR   0.014   0.001   TYR A 240 
 ARG   0.003   0.000   ARG A 338 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 170
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7068 (mm) cc_final: 0.6852 (mm)
REVERT: A   40 GLU cc_start: 0.7154 (mp0) cc_final: 0.6868 (mp0)
REVERT: A  164 MET cc_start: 0.6093 (mpp) cc_final: 0.5565 (mpp)
REVERT: A  185 ASP cc_start: 0.7013 (t70) cc_final: 0.6666 (t0)
REVERT: A  198 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7618 (mtmm)
REVERT: A  243 LEU cc_start: 0.8216 (tp) cc_final: 0.7955 (tt)
REVERT: A  282 GLU cc_start: 0.6430 (mp0) cc_final: 0.5844 (mp0)
REVERT: A  380 LYS cc_start: 0.7601 (mppt) cc_final: 0.7380 (mppt)
REVERT: A  386 ASP cc_start: 0.6972 (t70) cc_final: 0.6572 (t70)
REVERT: B   33 VAL cc_start: 0.8196 (t) cc_final: 0.7853 (m)
  outliers start: 3
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2087
  time to fit residues: 45.7475
Evaluate side-chains
  156 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 31 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0010
   chunk 44 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  29 HIS
A 172 HIS
A 357 GLN
** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.122107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.111668 restraints weight = 9433.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.114737 restraints weight = 4247.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.116657 restraints weight = 2312.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6390  Z= 0.236
  Angle     :  0.582  10.734   8683  Z= 0.293
  Chirality :  0.041   0.155    974
  Planarity :  0.005   0.064   1091
  Dihedral  : 12.108  88.990    932
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.46 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 11.38 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.27 (0.31), residues: 769
  helix:  1.00 (0.30), residues: 298
  sheet: -0.56 (0.44), residues: 151
  loop : -1.07 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  14 
 HIS   0.007   0.001   HIS A  29 
 PHE   0.012   0.002   PHE A 127 
 TYR   0.013   0.001   TYR A 240 
 ARG   0.006   0.000   ARG A 290 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 170
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7070 (mm) cc_final: 0.6817 (mm)
REVERT: A   40 GLU cc_start: 0.7282 (mp0) cc_final: 0.6922 (mp0)
REVERT: A  162 ASN cc_start: 0.6091 (m110) cc_final: 0.5788 (m110)
REVERT: A  185 ASP cc_start: 0.7029 (t70) cc_final: 0.6816 (t70)
REVERT: A  198 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7582 (mtmm)
REVERT: A  243 LEU cc_start: 0.8279 (tp) cc_final: 0.7932 (tt)
REVERT: A  327 ARG cc_start: 0.6300 (tmt170) cc_final: 0.6044 (tmt170)
REVERT: A  386 ASP cc_start: 0.6750 (t70) cc_final: 0.6512 (t70)
  outliers start: 5
  outliers final: 3
  residues processed: 174
  average time/residue: 0.2123
  time to fit residues: 46.8750
Evaluate side-chains
  163 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 160
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 SER
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  289 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 75 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0980
   chunk 51 optimal weight:    0.0980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A  29 HIS
A 172 HIS
A 357 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.122540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.111536 restraints weight = 9609.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.114817 restraints weight = 4233.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.116851 restraints weight = 2272.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6390  Z= 0.214
  Angle     :  0.576   8.289   8683  Z= 0.289
  Chirality :  0.040   0.149    974
  Planarity :  0.004   0.041   1091
  Dihedral  : 11.807  89.047    932
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.07 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.27 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.23 (0.31), residues: 769
  helix:  1.07 (0.30), residues: 298
  sheet: -0.59 (0.44), residues: 151
  loop : -1.05 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 458 
 HIS   0.005   0.001   HIS A  29 
 PHE   0.025   0.002   PHE A  45 
 TYR   0.010   0.001   TYR A 411 
 ARG   0.004   0.000   ARG A 290 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 164
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7169 (mm) cc_final: 0.6894 (mm)
REVERT: A   40 GLU cc_start: 0.7376 (mp0) cc_final: 0.6942 (mp0)
REVERT: A  162 ASN cc_start: 0.6154 (m110) cc_final: 0.5800 (m110)
REVERT: A  185 ASP cc_start: 0.6990 (t70) cc_final: 0.6775 (t70)
REVERT: A  198 LYS cc_start: 0.7972 (mtmm) cc_final: 0.7606 (mtmm)
REVERT: A  251 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.5947 (pttt)
REVERT: A  327 ARG cc_start: 0.6340 (tmt170) cc_final: 0.6036 (tmt170)
REVERT: A  386 ASP cc_start: 0.6862 (t70) cc_final: 0.6617 (t70)
  outliers start: 11
  outliers final: 4
  residues processed: 171
  average time/residue: 0.2102
  time to fit residues: 45.6464
Evaluate side-chains
  156 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 151
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 SER
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  251 LYS
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 41 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 172 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.119013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.107946 restraints weight = 9736.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.111192 restraints weight = 4335.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.113249 restraints weight = 2353.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6390  Z= 0.312
  Angle     :  0.605   8.312   8683  Z= 0.305
  Chirality :  0.042   0.162    974
  Planarity :  0.004   0.055   1091
  Dihedral  : 11.824  88.637    932
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.20 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 14.97 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.27 (0.31), residues: 769
  helix:  1.04 (0.30), residues: 299
  sheet: -0.61 (0.45), residues: 151
  loop : -1.08 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 458 
 HIS   0.002   0.000   HIS B 156 
 PHE   0.028   0.002   PHE A  45 
 TYR   0.013   0.001   TYR A 578 
 ARG   0.003   0.000   ARG A 290 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 GLU cc_start: 0.7403 (mp0) cc_final: 0.6921 (mp0)
REVERT: A  158 THR cc_start: 0.6827 (OUTLIER) cc_final: 0.6216 (t)
REVERT: A  162 ASN cc_start: 0.6108 (m110) cc_final: 0.5538 (m110)
REVERT: A  185 ASP cc_start: 0.6895 (t70) cc_final: 0.6627 (t70)
REVERT: A  198 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7701 (mtmm)
REVERT: A  243 LEU cc_start: 0.8209 (tp) cc_final: 0.7895 (tt)
REVERT: A  251 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.6016 (pttt)
REVERT: A  327 ARG cc_start: 0.6354 (tmt170) cc_final: 0.6009 (tmt170)
REVERT: A  362 TYR cc_start: 0.7348 (m-10) cc_final: 0.7134 (m-80)
REVERT: A  386 ASP cc_start: 0.6847 (t70) cc_final: 0.6566 (t70)
REVERT: B   93 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8200 (ttp80)
REVERT: B   95 LEU cc_start: 0.7917 (mt) cc_final: 0.7676 (mt)
  outliers start: 23
  outliers final: 15
  residues processed: 170
  average time/residue: 0.2297
  time to fit residues: 50.1258
Evaluate side-chains
  176 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 SER
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  251 LYS
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  523 GLN
Chi-restraints excluded: chain A residue  525 ASN
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  109 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0170
   chunk 21 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0770
   chunk 7 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0370
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.2254

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

Flipped N/Q/H residues before XYZ refinement:
A  60 HIS
A 357 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.122302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.111200 restraints weight = 9679.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.114483 restraints weight = 4312.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.116519 restraints weight = 2329.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6390  Z= 0.174
  Angle     :  0.558   7.711   8683  Z= 0.281
  Chirality :  0.039   0.141    974
  Planarity :  0.004   0.048   1091
  Dihedral  : 11.575  87.831    932
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.07 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.07 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.14 (0.31), residues: 769
  helix:  1.10 (0.30), residues: 300
  sheet: -0.66 (0.44), residues: 158
  loop : -0.89 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 458 
 HIS   0.004   0.001   HIS A  39 
 PHE   0.019   0.001   PHE A  45 
 TYR   0.011   0.001   TYR A 411 
 ARG   0.006   0.000   ARG A 290 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 HIS cc_start: 0.7174 (t-170) cc_final: 0.6875 (t-170)
REVERT: A   40 GLU cc_start: 0.7385 (mp0) cc_final: 0.7018 (mp0)
REVERT: A  158 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.6229 (t)
REVERT: A  162 ASN cc_start: 0.6044 (m110) cc_final: 0.5503 (m110)
REVERT: A  185 ASP cc_start: 0.6878 (t70) cc_final: 0.6598 (t70)
REVERT: A  198 LYS cc_start: 0.7997 (mtmm) cc_final: 0.7615 (mtmm)
REVERT: A  243 LEU cc_start: 0.8210 (tp) cc_final: 0.7870 (tt)
REVERT: A  251 LYS cc_start: 0.6394 (OUTLIER) cc_final: 0.5918 (pttt)
REVERT: A  282 GLU cc_start: 0.6591 (mp0) cc_final: 0.5796 (mp0)
REVERT: A  386 ASP cc_start: 0.6868 (t70) cc_final: 0.6614 (t70)
REVERT: A  600 ILE cc_start: 0.8451 (tt) cc_final: 0.8238 (tt)
  outliers start: 19
  outliers final: 10
  residues processed: 172
  average time/residue: 0.2032
  time to fit residues: 44.6142
Evaluate side-chains
  169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 157
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   56 SER
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain A residue  251 LYS
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  525 ASN
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  109 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 67 optimal weight:    0.3980
   chunk 1 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0470
   chunk 53 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
A  60 HIS
B 156 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.120728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.109776 restraints weight = 9563.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.112995 restraints weight = 4314.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.114962 restraints weight = 2358.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6390  Z= 0.251
  Angle     :  0.592   8.032   8683  Z= 0.298
  Chirality :  0.041   0.175    974
  Planarity :  0.004   0.060   1091
  Dihedral  : 11.600  87.314    932
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.81 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.66 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.18 (0.31), residues: 769
  helix:  1.11 (0.30), residues: 299
  sheet: -0.77 (0.44), residues: 158
  loop : -0.90 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 458 
 HIS   0.007   0.001   HIS A  60 
 PHE   0.015   0.002   PHE A  45 
 TYR   0.010   0.001   TYR A 578 
 ARG   0.005   0.000   ARG A 290 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 156
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 HIS cc_start: 0.7238 (t-170) cc_final: 0.6949 (t-170)
REVERT: A   40 GLU cc_start: 0.7372 (mp0) cc_final: 0.6973 (mp0)
REVERT: A  158 THR cc_start: 0.6845 (OUTLIER) cc_final: 0.6214 (t)
REVERT: A  162 ASN cc_start: 0.6052 (m110) cc_final: 0.5508 (m110)
REVERT: A  198 LYS cc_start: 0.7996 (mtmm) cc_final: 0.7615 (mtmm)
REVERT: A  243 LEU cc_start: 0.8209 (tp) cc_final: 0.7852 (tt)
REVERT: A  251 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5914 (pttt)
REVERT: A  282 GLU cc_start: 0.6310 (mp0) cc_final: 0.5931 (mp0)
REVERT: A  362 TYR cc_start: 0.7341 (m-10) cc_final: 0.6812 (m-80)
REVERT: A  386 ASP cc_start: 0.6852 (t70) cc_final: 0.6582 (t70)
REVERT: B   93 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7736 (ttp80)
REVERT: B  114 MET cc_start: 0.7555 (mmp) cc_final: 0.7288 (mmm)
  outliers start: 23
  outliers final: 16
  residues processed: 168
  average time/residue: 0.2190
  time to fit residues: 46.4187
Evaluate side-chains
  174 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  251 LYS
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  525 ASN
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  141 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0770
   chunk 58 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A  60 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.120209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.109261 restraints weight = 9627.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.112502 restraints weight = 4332.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.114517 restraints weight = 2361.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6390  Z= 0.263
  Angle     :  0.602   8.770   8683  Z= 0.303
  Chirality :  0.041   0.170    974
  Planarity :  0.004   0.054   1091
  Dihedral  : 11.611  86.849    932
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.42 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 17.37 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.21 (0.31), residues: 769
  helix:  1.09 (0.30), residues: 299
  sheet: -0.80 (0.44), residues: 158
  loop : -0.91 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 458 
 HIS   0.006   0.001   HIS A  60 
 PHE   0.029   0.002   PHE A  45 
 TYR   0.010   0.001   TYR A 578 
 ARG   0.004   0.000   ARG A 290 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 HIS cc_start: 0.7241 (t-170) cc_final: 0.6956 (t-170)
REVERT: A   40 GLU cc_start: 0.7372 (mp0) cc_final: 0.6988 (mp0)
REVERT: A  158 THR cc_start: 0.6838 (OUTLIER) cc_final: 0.6206 (t)
REVERT: A  162 ASN cc_start: 0.6024 (m110) cc_final: 0.5497 (m110)
REVERT: A  198 LYS cc_start: 0.8007 (mtmm) cc_final: 0.7631 (mtmm)
REVERT: A  243 LEU cc_start: 0.8210 (tp) cc_final: 0.7862 (tt)
REVERT: A  251 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5927 (pttt)
REVERT: A  362 TYR cc_start: 0.7336 (m-10) cc_final: 0.6806 (m-80)
REVERT: A  386 ASP cc_start: 0.6869 (t70) cc_final: 0.6610 (t70)
REVERT: B   93 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7766 (ttp80)
REVERT: B  114 MET cc_start: 0.7552 (mmp) cc_final: 0.7301 (mmm)
  outliers start: 26
  outliers final: 19
  residues processed: 167
  average time/residue: 0.2320
  time to fit residues: 48.7817
Evaluate side-chains
  172 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  251 LYS
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  523 GLN
Chi-restraints excluded: chain A residue  525 ASN
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  109 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3501 r_free = 0.3501 target = 0.118422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.107473 restraints weight = 9677.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.110744 restraints weight = 4340.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.112754 restraints weight = 2347.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6390  Z= 0.359
  Angle     :  0.644   9.425   8683  Z= 0.324
  Chirality :  0.044   0.196    974
  Planarity :  0.004   0.051   1091
  Dihedral  : 11.726  86.884    932
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.81 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 17.81 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.42 (0.31), residues: 769
  helix:  0.86 (0.30), residues: 306
  sheet: -0.85 (0.44), residues: 158
  loop : -1.05 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 458 
 HIS   0.008   0.001   HIS A  60 
 PHE   0.030   0.002   PHE A  45 
 TYR   0.012   0.001   TYR A 426 
 ARG   0.004   0.000   ARG A 290 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 HIS cc_start: 0.7297 (t-170) cc_final: 0.6832 (t70)
REVERT: A   40 GLU cc_start: 0.7391 (mp0) cc_final: 0.6895 (mp0)
REVERT: A  158 THR cc_start: 0.6877 (OUTLIER) cc_final: 0.6238 (t)
REVERT: A  162 ASN cc_start: 0.6031 (m110) cc_final: 0.5490 (m110)
REVERT: A  198 LYS cc_start: 0.8061 (mtmm) cc_final: 0.7706 (mtmm)
REVERT: A  362 TYR cc_start: 0.7361 (m-10) cc_final: 0.6814 (m-80)
REVERT: A  386 ASP cc_start: 0.6874 (t70) cc_final: 0.6601 (t70)
REVERT: B   64 LYS cc_start: 0.8003 (mppt) cc_final: 0.7777 (mppt)
REVERT: B   93 ARG cc_start: 0.8319 (ttp80) cc_final: 0.8063 (ttp80)
REVERT: B  114 MET cc_start: 0.7574 (mmp) cc_final: 0.7343 (mmm)
  outliers start: 27
  outliers final: 20
  residues processed: 174
  average time/residue: 0.2170
  time to fit residues: 48.0870
Evaluate side-chains
  180 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 159
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  251 LYS
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  523 GLN
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue  109 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 67 optimal weight:    0.3980
   chunk 65 optimal weight:    0.0470
   chunk 39 optimal weight:    0.0970
   chunk 12 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0000
   chunk 53 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.2480

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

Flipped N/Q/H residues before XYZ refinement:
B 156 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.121742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.110660 restraints weight = 9595.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.113835 restraints weight = 4310.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.115952 restraints weight = 2377.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6390  Z= 0.186
  Angle     :  0.610  10.884   8683  Z= 0.301
  Chirality :  0.040   0.154    974
  Planarity :  0.004   0.050   1091
  Dihedral  : 11.550  85.961    932
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.07 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 20.21 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.15 (0.32), residues: 769
  helix:  1.05 (0.30), residues: 299
  sheet: -0.78 (0.45), residues: 158
  loop : -0.77 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 458 
 HIS   0.004   0.001   HIS A  60 
 PHE   0.017   0.002   PHE A  45 
 TYR   0.010   0.001   TYR A 411 
 ARG   0.004   0.000   ARG A 290 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 HIS cc_start: 0.7203 (t-170) cc_final: 0.6784 (t70)
REVERT: A   40 GLU cc_start: 0.7340 (mp0) cc_final: 0.6972 (mp0)
REVERT: A   64 LEU cc_start: 0.8230 (tt) cc_final: 0.7989 (tp)
REVERT: A  158 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6223 (t)
REVERT: A  162 ASN cc_start: 0.5960 (m110) cc_final: 0.5452 (m110)
REVERT: A  185 ASP cc_start: 0.6786 (t70) cc_final: 0.6436 (t70)
REVERT: A  198 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7589 (mtmm)
REVERT: A  243 LEU cc_start: 0.8213 (tp) cc_final: 0.7895 (tt)
REVERT: A  251 LYS cc_start: 0.6249 (OUTLIER) cc_final: 0.5930 (pttt)
REVERT: A  362 TYR cc_start: 0.7302 (m-10) cc_final: 0.6760 (m-80)
REVERT: A  386 ASP cc_start: 0.6872 (t70) cc_final: 0.6624 (t70)
REVERT: B  114 MET cc_start: 0.7504 (mmp) cc_final: 0.7264 (mmm)
  outliers start: 19
  outliers final: 13
  residues processed: 172
  average time/residue: 0.2203
  time to fit residues: 48.6988
Evaluate side-chains
  170 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  251 LYS
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  525 ASN
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  109 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0370
   chunk 3 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0970
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.5056

-------------------------------------------------------------------------------
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 = 0.3525 r_free = 0.3525 target = 0.120210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.109080 restraints weight = 9679.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.112386 restraints weight = 4338.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.114452 restraints weight = 2361.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6390  Z= 0.253
  Angle     :  0.634   8.907   8683  Z= 0.313
  Chirality :  0.042   0.193    974
  Planarity :  0.004   0.068   1091
  Dihedral  : 11.599  86.400    932
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.94 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 20.36 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.18 (0.31), residues: 769
  helix:  1.07 (0.30), residues: 299
  sheet: -0.80 (0.45), residues: 158
  loop : -0.82 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 458 
 HIS   0.002   0.000   HIS A  39 
 PHE   0.021   0.002   PHE A  45 
 TYR   0.018   0.001   TYR A  41 
 ARG   0.004   0.000   ARG A 290 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 HIS cc_start: 0.7239 (t-170) cc_final: 0.6809 (t70)
REVERT: A   40 GLU cc_start: 0.7328 (mp0) cc_final: 0.6872 (mp0)
REVERT: A   51 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7311 (ptm-80)
REVERT: A  158 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.6236 (t)
REVERT: A  162 ASN cc_start: 0.5962 (m110) cc_final: 0.5459 (m110)
REVERT: A  198 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7629 (mtmm)
REVERT: A  243 LEU cc_start: 0.8209 (tp) cc_final: 0.7913 (tt)
REVERT: A  251 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.5950 (pttt)
REVERT: A  362 TYR cc_start: 0.7314 (m-10) cc_final: 0.6763 (m-80)
REVERT: A  386 ASP cc_start: 0.6890 (t70) cc_final: 0.6611 (t70)
REVERT: B  114 MET cc_start: 0.7529 (mmp) cc_final: 0.7301 (mmm)
  outliers start: 19
  outliers final: 14
  residues processed: 163
  average time/residue: 0.2162
  time to fit residues: 45.0512
Evaluate side-chains
  169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  251 LYS
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  525 ASN
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  141 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 67 optimal weight:    0.3980
   chunk 37 optimal weight:    0.0770
   chunk 8 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.3522 r_free = 0.3522 target = 0.119936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.108749 restraints weight = 9763.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.112083 restraints weight = 4382.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.114141 restraints weight = 2384.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6390  Z= 0.267
  Angle     :  0.642   8.923   8683  Z= 0.318
  Chirality :  0.042   0.199    974
  Planarity :  0.004   0.067   1091
  Dihedral  : 11.641  86.556    932
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.07 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.81 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.28 (0.31), residues: 769
  helix:  0.95 (0.30), residues: 306
  sheet: -0.69 (0.45), residues: 152
  loop : -0.99 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.000   HIS B 156 
 PHE   0.021   0.002   PHE A  45 
 TYR   0.052   0.002   TYR A  41 
 ARG   0.005   0.000   ARG A 472 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2477.40 seconds
wall clock time: 43 minutes 33.36 seconds (2613.36 seconds total)