Starting phenix.real_space_refine
on Wed Sep 17 06:36:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9caj_45393/09_2025/9caj_45393_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9caj_45393/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9caj_45393/09_2025/9caj_45393_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9caj_45393/09_2025/9caj_45393_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9caj_45393/09_2025/9caj_45393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9caj_45393/09_2025/9caj_45393.map"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.82, per 1000 atoms: 0.29
  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: 0.54
  Conformation dependent library (CDL) restraints added in 400.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.67
  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: 1.04

  Time building geometry restraints manager: 0.74 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:             2.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     8.620
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.920
-------------------------------------------------------------------------------
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= 0.174
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG A 338 
 TYR   0.014   0.001   TYR A 240 
 PHE   0.011   0.001   PHE B  52 
 TRP   0.007   0.001   TRP A 458 
 HIS   0.007   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6390)
  covalent geometry    : angle       0.66310 ( 8683)
  hydrogen bonds       : bond        0.08452 (  258)
  hydrogen bonds       : angle       4.86236 (  732)

*********************** 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  : 0.249 
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: 0.0932
  time to fit residues: 20.4252
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  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 218 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 = 0.3508 r_free = 0.3508 target = 0.119038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.108381 restraints weight = 9647.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.111544 restraints weight = 4297.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.113455 restraints weight = 2320.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.114669 restraints weight = 1442.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.115476 restraints weight = 990.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   6390  Z= 0.257
  Angle     :  0.637  10.803   8683  Z= 0.323
  Chirality :  0.044   0.172    974
  Planarity :  0.005   0.068   1091
  Dihedral  : 12.188  89.995    932
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.59 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 11.23 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.31), residues: 769
  helix:  0.83 (0.30), residues: 298
  sheet: -0.68 (0.44), residues: 158
  loop : -1.13 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 290 
 TYR   0.019   0.002   TYR A 240 
 PHE   0.015   0.002   PHE A 127 
 TRP   0.010   0.001   TRP A 458 
 HIS   0.006   0.001   HIS A  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 ( 6390)
  covalent geometry    : angle       0.63704 ( 8683)
  hydrogen bonds       : bond        0.04319 (  258)
  hydrogen bonds       : angle       4.61642 (  732)

*********************** 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
  181 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 175
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7227 (mm) cc_final: 0.7001 (mm)
REVERT: A   40 GLU cc_start: 0.7359 (mp0) cc_final: 0.6971 (mp0)
REVERT: A  162 ASN cc_start: 0.6080 (m110) cc_final: 0.5746 (m110)
REVERT: A  198 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7707 (mtmm)
REVERT: A  327 ARG cc_start: 0.6313 (tmt170) cc_final: 0.6007 (tmt170)
REVERT: A  380 LYS cc_start: 0.7628 (mppt) cc_final: 0.7416 (mppt)
REVERT: A  386 ASP cc_start: 0.6731 (t70) cc_final: 0.6484 (t70)
REVERT: A  438 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6939 (mm-30)
REVERT: A  593 PHE cc_start: 0.8171 (t80) cc_final: 0.7966 (t80)
REVERT: B   57 ILE cc_start: 0.8134 (tp) cc_final: 0.7928 (tp)
  outliers start: 6
  outliers final: 3
  residues processed: 177
  average time/residue: 0.0961
  time to fit residues: 21.6497
Evaluate side-chains
  169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 166
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 LEU
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 14 optimal weight:    0.1980
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 72 optimal weight:    0.2980
   chunk 35 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 57 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   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 218 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.120948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.110035 restraints weight = 9492.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.113214 restraints weight = 4182.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.115233 restraints weight = 2256.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.116459 restraints weight = 1388.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.117273 restraints weight = 952.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6390  Z= 0.148
  Angle     :  0.589   8.877   8683  Z= 0.295
  Chirality :  0.041   0.154    974
  Planarity :  0.004   0.045   1091
  Dihedral  : 11.917  88.853    932
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.81 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.67 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.32), residues: 769
  helix:  0.90 (0.30), residues: 299
  sheet: -0.72 (0.44), residues: 158
  loop : -1.02 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  93 
 TYR   0.010   0.001   TYR A 411 
 PHE   0.016   0.002   PHE A 127 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.004   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6390)
  covalent geometry    : angle       0.58871 ( 8683)
  hydrogen bonds       : bond        0.03503 (  258)
  hydrogen bonds       : angle       4.43098 (  732)

*********************** 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
  183 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 169
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7217 (mm) cc_final: 0.6966 (mm)
REVERT: A   40 GLU cc_start: 0.7389 (mp0) cc_final: 0.6915 (mp0)
REVERT: A  158 THR cc_start: 0.6828 (OUTLIER) cc_final: 0.6252 (t)
REVERT: A  162 ASN cc_start: 0.6073 (m110) cc_final: 0.5551 (m110)
REVERT: A  198 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7704 (mtmm)
REVERT: A  243 LEU cc_start: 0.8239 (tp) cc_final: 0.7890 (tt)
REVERT: A  251 LYS cc_start: 0.6300 (OUTLIER) cc_final: 0.5987 (pttt)
REVERT: A  282 GLU cc_start: 0.6337 (mp0) cc_final: 0.5808 (mp0)
REVERT: A  327 ARG cc_start: 0.6322 (tmt170) cc_final: 0.5993 (tmt170)
REVERT: A  380 LYS cc_start: 0.7647 (mppt) cc_final: 0.7418 (mppt)
REVERT: A  386 ASP cc_start: 0.6796 (t70) cc_final: 0.6555 (t70)
REVERT: A  438 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6929 (mm-30)
REVERT: B   93 ARG cc_start: 0.8495 (ttp80) cc_final: 0.7740 (ttp80)
REVERT: B   95 LEU cc_start: 0.7880 (mt) cc_final: 0.7674 (mp)
REVERT: B  117 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7823 (mm)
  outliers start: 14
  outliers final: 3
  residues processed: 177
  average time/residue: 0.0953
  time to fit residues: 21.4769
Evaluate side-chains
  170 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 164
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  246 LYS
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 B residue  117 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 14 optimal weight:    0.0470
   chunk 49 optimal weight:    0.0670
   chunk 19 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.3016

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.121373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.110369 restraints weight = 9609.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.113626 restraints weight = 4288.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.115660 restraints weight = 2326.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.116949 restraints weight = 1436.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.117774 restraints weight = 974.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6390  Z= 0.127
  Angle     :  0.575   7.933   8683  Z= 0.287
  Chirality :  0.040   0.144    974
  Planarity :  0.004   0.038   1091
  Dihedral  : 11.745  88.379    932
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.33 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.92 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.31), residues: 769
  helix:  1.02 (0.30), residues: 299
  sheet: -0.68 (0.45), residues: 151
  loop : -1.08 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  93 
 TYR   0.010   0.001   TYR A 411 
 PHE   0.015   0.001   PHE A 127 
 TRP   0.007   0.001   TRP A 458 
 HIS   0.005   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6390)
  covalent geometry    : angle       0.57507 ( 8683)
  hydrogen bonds       : bond        0.03204 (  258)
  hydrogen bonds       : angle       4.33637 (  732)

*********************** 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
  183 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 169
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7174 (mm) cc_final: 0.6958 (mm)
REVERT: A   40 GLU cc_start: 0.7343 (mp0) cc_final: 0.6921 (mp0)
REVERT: A  148 PHE cc_start: 0.8114 (m-80) cc_final: 0.7896 (m-10)
REVERT: A  162 ASN cc_start: 0.5992 (m110) cc_final: 0.5656 (m110)
REVERT: A  198 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7647 (mtmm)
REVERT: A  243 LEU cc_start: 0.8225 (tp) cc_final: 0.7872 (tt)
REVERT: A  251 LYS cc_start: 0.6222 (OUTLIER) cc_final: 0.5923 (pttt)
REVERT: A  362 TYR cc_start: 0.7319 (m-10) cc_final: 0.6852 (m-80)
REVERT: A  380 LYS cc_start: 0.7604 (mppt) cc_final: 0.7402 (mppt)
REVERT: A  386 ASP cc_start: 0.6752 (t70) cc_final: 0.6500 (t70)
REVERT: B   93 ARG cc_start: 0.8466 (ttp80) cc_final: 0.7768 (ttp80)
REVERT: B   94 MET cc_start: 0.7664 (ttm) cc_final: 0.7363 (ttm)
  outliers start: 14
  outliers final: 6
  residues processed: 176
  average time/residue: 0.0898
  time to fit residues: 20.2341
Evaluate side-chains
  170 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 163
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
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  233 GLN
Chi-restraints excluded: chain A residue  251 LYS
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  141 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 16 optimal weight:    0.2980
   chunk 51 optimal weight:    0.0870
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 = 0.3517 r_free = 0.3517 target = 0.119554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.108449 restraints weight = 9788.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.111744 restraints weight = 4333.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.113791 restraints weight = 2343.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.115049 restraints weight = 1447.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.115890 restraints weight = 994.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6390  Z= 0.191
  Angle     :  0.600   7.991   8683  Z= 0.302
  Chirality :  0.042   0.163    974
  Planarity :  0.004   0.058   1091
  Dihedral  : 11.824  88.136    932
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.20 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 16.32 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.31), residues: 769
  helix:  0.98 (0.30), residues: 299
  sheet: -0.70 (0.44), residues: 151
  loop : -1.09 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 290 
 TYR   0.011   0.001   TYR A 578 
 PHE   0.017   0.002   PHE A 127 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.008   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 6390)
  covalent geometry    : angle       0.60050 ( 8683)
  hydrogen bonds       : bond        0.03714 (  258)
  hydrogen bonds       : angle       4.44666 (  732)

*********************** 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
  187 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 GLU cc_start: 0.7368 (mp0) cc_final: 0.6901 (mp0)
REVERT: A  158 THR cc_start: 0.6865 (OUTLIER) cc_final: 0.6233 (t)
REVERT: A  162 ASN cc_start: 0.6004 (m110) cc_final: 0.5460 (m110)
REVERT: A  198 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7688 (mtmm)
REVERT: A  243 LEU cc_start: 0.8219 (tp) cc_final: 0.7862 (tt)
REVERT: A  251 LYS cc_start: 0.6371 (OUTLIER) cc_final: 0.6036 (pttt)
REVERT: A  362 TYR cc_start: 0.7359 (m-10) cc_final: 0.6831 (m-80)
REVERT: A  380 LYS cc_start: 0.7634 (mppt) cc_final: 0.7421 (mppt)
REVERT: A  386 ASP cc_start: 0.6831 (t70) cc_final: 0.6573 (t70)
REVERT: B   93 ARG cc_start: 0.8441 (ttp80) cc_final: 0.7894 (ttp-170)
REVERT: B   94 MET cc_start: 0.7569 (ttm) cc_final: 0.7364 (ttm)
  outliers start: 25
  outliers final: 15
  residues processed: 174
  average time/residue: 0.0901
  time to fit residues: 20.0189
Evaluate side-chains
  177 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  251 LYS
Chi-restraints excluded: chain A residue  286 GLU
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 B residue   33 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0970
   chunk 7 optimal weight:    0.2980
   chunk 11 optimal weight:    0.5980
   chunk 45 optimal weight:    0.1980
   chunk 20 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.3178

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.120947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.110015 restraints weight = 9650.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.113279 restraints weight = 4307.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.115294 restraints weight = 2330.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.116576 restraints weight = 1438.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.117368 restraints weight = 979.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6390  Z= 0.129
  Angle     :  0.576   8.084   8683  Z= 0.287
  Chirality :  0.040   0.153    974
  Planarity :  0.004   0.051   1091
  Dihedral  : 11.695  87.684    932
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.20 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.31), residues: 769
  helix:  1.02 (0.30), residues: 299
  sheet: -0.58 (0.45), residues: 150
  loop : -0.94 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 290 
 TYR   0.010   0.001   TYR A 411 
 PHE   0.014   0.001   PHE A 127 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.011   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6390)
  covalent geometry    : angle       0.57581 ( 8683)
  hydrogen bonds       : bond        0.03247 (  258)
  hydrogen bonds       : angle       4.34160 (  732)

*********************** 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
  188 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 HIS cc_start: 0.7168 (t-170) cc_final: 0.6752 (t70)
REVERT: A   40 GLU cc_start: 0.7341 (mp0) cc_final: 0.6960 (mp0)
REVERT: A  144 GLU cc_start: 0.7235 (pm20) cc_final: 0.6883 (pm20)
REVERT: A  148 PHE cc_start: 0.8176 (m-80) cc_final: 0.7927 (m-10)
REVERT: A  158 THR cc_start: 0.6831 (OUTLIER) cc_final: 0.6213 (t)
REVERT: A  159 ASP cc_start: 0.8007 (m-30) cc_final: 0.7761 (m-30)
REVERT: A  162 ASN cc_start: 0.5966 (m110) cc_final: 0.5449 (m110)
REVERT: A  198 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7613 (mtmm)
REVERT: A  243 LEU cc_start: 0.8217 (tp) cc_final: 0.7849 (tt)
REVERT: A  251 LYS cc_start: 0.6315 (OUTLIER) cc_final: 0.6006 (pttt)
REVERT: A  362 TYR cc_start: 0.7356 (m-10) cc_final: 0.6832 (m-80)
REVERT: A  380 LYS cc_start: 0.7611 (mppt) cc_final: 0.7400 (mppt)
REVERT: A  386 ASP cc_start: 0.6811 (t70) cc_final: 0.6560 (t70)
REVERT: A  606 LEU cc_start: 0.8556 (tp) cc_final: 0.8354 (tt)
REVERT: B   93 ARG cc_start: 0.8297 (ttp80) cc_final: 0.8040 (ttp-110)
  outliers start: 22
  outliers final: 15
  residues processed: 177
  average time/residue: 0.0925
  time to fit residues: 20.7788
Evaluate side-chains
  181 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
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  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  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 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 26 optimal weight:    0.9990
   chunk 19 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0970
   chunk 15 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.3522 r_free = 0.3522 target = 0.120103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.109099 restraints weight = 9695.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.112341 restraints weight = 4347.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.114390 restraints weight = 2375.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.115665 restraints weight = 1473.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.116474 restraints weight = 1006.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6390  Z= 0.163
  Angle     :  0.588   8.274   8683  Z= 0.295
  Chirality :  0.041   0.161    974
  Planarity :  0.004   0.047   1091
  Dihedral  : 11.704  87.022    932
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.20 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 17.81 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.31), residues: 769
  helix:  1.04 (0.30), residues: 299
  sheet: -0.54 (0.46), residues: 150
  loop : -0.93 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 290 
 TYR   0.014   0.001   TYR A  41 
 PHE   0.036   0.002   PHE A  45 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.009   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 6390)
  covalent geometry    : angle       0.58764 ( 8683)
  hydrogen bonds       : bond        0.03435 (  258)
  hydrogen bonds       : angle       4.38255 (  732)

*********************** 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
  190 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 GLU cc_start: 0.7355 (mp0) cc_final: 0.6983 (mp0)
REVERT: A  144 GLU cc_start: 0.7253 (pm20) cc_final: 0.6868 (pm20)
REVERT: A  158 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.6231 (t)
REVERT: A  162 ASN cc_start: 0.5955 (m110) cc_final: 0.5440 (m110)
REVERT: A  198 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7655 (mtmm)
REVERT: A  251 LYS cc_start: 0.6350 (OUTLIER) cc_final: 0.6020 (pttt)
REVERT: A  362 TYR cc_start: 0.7363 (m-10) cc_final: 0.6840 (m-80)
REVERT: A  380 LYS cc_start: 0.7610 (mppt) cc_final: 0.7385 (mppt)
REVERT: A  386 ASP cc_start: 0.6824 (t70) cc_final: 0.6574 (t70)
REVERT: B   93 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7892 (ttp-170)
  outliers start: 25
  outliers final: 17
  residues processed: 178
  average time/residue: 0.0978
  time to fit residues: 22.1125
Evaluate side-chains
  176 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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  112 ILE
Chi-restraints excluded: chain A residue  158 THR
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  376 ASN
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  581 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0870
   chunk 45 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0980
   chunk 4 optimal weight:    0.1980
   chunk 73 optimal weight:    0.4980
   overall best weight:    0.2958

-------------------------------------------------------------------------------
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 = 0.3541 r_free = 0.3541 target = 0.121457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.110284 restraints weight = 9697.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.113613 restraints weight = 4349.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.115652 restraints weight = 2358.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.116915 restraints weight = 1460.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.117776 restraints weight = 1007.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6390  Z= 0.123
  Angle     :  0.584   8.570   8683  Z= 0.289
  Chirality :  0.040   0.149    974
  Planarity :  0.004   0.065   1091
  Dihedral  : 11.614  86.192    932
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.94 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.86 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.31), residues: 769
  helix:  1.09 (0.30), residues: 300
  sheet: -0.45 (0.47), residues: 137
  loop : -0.90 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 290 
 TYR   0.040   0.001   TYR A  41 
 PHE   0.038   0.002   PHE A  45 
 TRP   0.009   0.001   TRP A 458 
 HIS   0.008   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6390)
  covalent geometry    : angle       0.58426 ( 8683)
  hydrogen bonds       : bond        0.03115 (  258)
  hydrogen bonds       : angle       4.35236 (  732)

*********************** 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
  183 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 HIS cc_start: 0.7179 (t-170) cc_final: 0.6719 (t70)
REVERT: A   40 GLU cc_start: 0.7230 (mp0) cc_final: 0.6806 (mp0)
REVERT: A   75 LYS cc_start: 0.8393 (mmmt) cc_final: 0.8127 (mmmm)
REVERT: A  144 GLU cc_start: 0.7233 (pm20) cc_final: 0.6840 (pm20)
REVERT: A  158 THR cc_start: 0.6835 (OUTLIER) cc_final: 0.6235 (t)
REVERT: A  162 ASN cc_start: 0.5940 (m110) cc_final: 0.5422 (m110)
REVERT: A  198 LYS cc_start: 0.7963 (mtmm) cc_final: 0.7590 (mtmm)
REVERT: A  251 LYS cc_start: 0.6326 (OUTLIER) cc_final: 0.5897 (pttt)
REVERT: A  362 TYR cc_start: 0.7337 (m-10) cc_final: 0.6818 (m-80)
REVERT: A  380 LYS cc_start: 0.7615 (mppt) cc_final: 0.7374 (mppt)
REVERT: A  386 ASP cc_start: 0.6848 (t70) cc_final: 0.6569 (t70)
REVERT: B   93 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8136 (ttp-110)
  outliers start: 22
  outliers final: 14
  residues processed: 172
  average time/residue: 0.0941
  time to fit residues: 20.6126
Evaluate side-chains
  179 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 163
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
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  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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 46 optimal weight:    0.3980
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 7 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0770
   chunk 57 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 69 optimal weight:    0.1980
   overall best weight:    0.3338

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.121565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.110492 restraints weight = 9734.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.113708 restraints weight = 4398.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.115774 restraints weight = 2419.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.117067 restraints weight = 1496.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.117945 restraints weight = 1019.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6390  Z= 0.129
  Angle     :  0.592   9.424   8683  Z= 0.293
  Chirality :  0.040   0.150    974
  Planarity :  0.004   0.067   1091
  Dihedral  : 11.547  86.280    932
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.20 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 19.31 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.31), residues: 769
  helix:  1.12 (0.30), residues: 299
  sheet: -0.42 (0.47), residues: 143
  loop : -0.85 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 290 
 TYR   0.061   0.002   TYR A  41 
 PHE   0.014   0.001   PHE A 127 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.009   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6390)
  covalent geometry    : angle       0.59205 ( 8683)
  hydrogen bonds       : bond        0.03180 (  258)
  hydrogen bonds       : angle       4.40524 (  732)

*********************** 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
  182 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 HIS cc_start: 0.7187 (t-170) cc_final: 0.6787 (t70)
REVERT: A   40 GLU cc_start: 0.7220 (mp0) cc_final: 0.6829 (mp0)
REVERT: A   51 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.7265 (ttm-80)
REVERT: A   75 LYS cc_start: 0.8340 (mmmt) cc_final: 0.8079 (mmmm)
REVERT: A  144 GLU cc_start: 0.7200 (pm20) cc_final: 0.6847 (pm20)
REVERT: A  158 THR cc_start: 0.6831 (OUTLIER) cc_final: 0.6210 (t)
REVERT: A  162 ASN cc_start: 0.5930 (m110) cc_final: 0.5419 (m110)
REVERT: A  184 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6704 (mp)
REVERT: A  198 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7619 (mtmm)
REVERT: A  251 LYS cc_start: 0.6176 (OUTLIER) cc_final: 0.5889 (pttt)
REVERT: A  380 LYS cc_start: 0.7618 (mppt) cc_final: 0.7381 (mppt)
REVERT: A  386 ASP cc_start: 0.6802 (t70) cc_final: 0.6547 (t70)
REVERT: B   93 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8242 (ttp80)
  outliers start: 19
  outliers final: 11
  residues processed: 170
  average time/residue: 0.0985
  time to fit residues: 21.3345
Evaluate side-chains
  173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 159
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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  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 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 18 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 73 optimal weight:    0.2980
   chunk 7 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 69 optimal weight:    0.4980
   chunk 67 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 172 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 = 0.3523 r_free = 0.3523 target = 0.120234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.109209 restraints weight = 9700.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.112482 restraints weight = 4379.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.114536 restraints weight = 2380.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.115782 restraints weight = 1464.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.116647 restraints weight = 1006.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.2055

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= 0.173
  Angle     :  0.620   8.586   8683  Z= 0.307
  Chirality :  0.041   0.162    974
  Planarity :  0.004   0.069   1091
  Dihedral  : 11.609  86.705    932
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.46 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 20.06 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.31), residues: 769
  helix:  1.08 (0.30), residues: 298
  sheet: -0.48 (0.47), residues: 143
  loop : -0.92 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 290 
 TYR   0.053   0.002   TYR A  41 
 PHE   0.013   0.002   PHE A 127 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.011   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6390)
  covalent geometry    : angle       0.62036 ( 8683)
  hydrogen bonds       : bond        0.03490 (  258)
  hydrogen bonds       : angle       4.44409 (  732)

********************** 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
  176 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 HIS cc_start: 0.7200 (t-170) cc_final: 0.6784 (t70)
REVERT: A   40 GLU cc_start: 0.7254 (mp0) cc_final: 0.6873 (mp0)
REVERT: A   51 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7286 (ttm-80)
REVERT: A   75 LYS cc_start: 0.8340 (mmmt) cc_final: 0.8085 (mmmm)
REVERT: A  144 GLU cc_start: 0.7224 (pm20) cc_final: 0.6876 (pt0)
REVERT: A  158 THR cc_start: 0.6870 (OUTLIER) cc_final: 0.6261 (t)
REVERT: A  162 ASN cc_start: 0.5928 (m110) cc_final: 0.5423 (m110)
REVERT: A  184 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6689 (mp)
REVERT: A  198 LYS cc_start: 0.8014 (mtmm) cc_final: 0.7639 (mtmm)
REVERT: A  251 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5848 (pttt)
REVERT: A  296 GLN cc_start: 0.7637 (tt0) cc_final: 0.7433 (tt0)
REVERT: A  380 LYS cc_start: 0.7633 (mppt) cc_final: 0.7388 (mppt)
REVERT: A  386 ASP cc_start: 0.6838 (t70) cc_final: 0.6565 (t70)
REVERT: B   93 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8201 (ttp80)
  outliers start: 19
  outliers final: 13
  residues processed: 164
  average time/residue: 0.0934
  time to fit residues: 19.3569
Evaluate side-chains
  172 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
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  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  376 ASN
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  483 MET
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 53 optimal weight:    0.7980
   chunk 73 optimal weight:    0.4980
   chunk 43 optimal weight:    0.7980
   chunk 9 optimal weight:    0.2980
   chunk 12 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0980
   chunk 44 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 38 optimal weight:    0.1980
   overall best weight:    0.3380

-------------------------------------------------------------------------------
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 = 0.3541 r_free = 0.3541 target = 0.121656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.110811 restraints weight = 9785.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.114019 restraints weight = 4439.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.116077 restraints weight = 2435.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.117335 restraints weight = 1501.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.118149 restraints weight = 1027.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6390  Z= 0.130
  Angle     :  0.599   8.642   8683  Z= 0.296
  Chirality :  0.040   0.159    974
  Planarity :  0.004   0.067   1091
  Dihedral  : 11.524  86.270    932
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 20.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.31), residues: 769
  helix:  1.11 (0.30), residues: 299
  sheet: -0.48 (0.46), residues: 143
  loop : -0.86 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 472 
 TYR   0.045   0.001   TYR A  41 
 PHE   0.012   0.001   PHE A 127 
 TRP   0.009   0.001   TRP A 458 
 HIS   0.004   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6390)
  covalent geometry    : angle       0.59926 ( 8683)
  hydrogen bonds       : bond        0.03210 (  258)
  hydrogen bonds       : angle       4.39570 (  732)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1313.72 seconds
wall clock time: 23 minutes 24.47 seconds (1404.47 seconds total)