Starting phenix.real_space_refine
on Fri Aug 22 17:40:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i4h_35173/08_2025/8i4h_35173.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i4h_35173/08_2025/8i4h_35173.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i4h_35173/08_2025/8i4h_35173.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i4h_35173/08_2025/8i4h_35173.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i4h_35173/08_2025/8i4h_35173.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i4h_35173/08_2025/8i4h_35173.cif"
  }
  resolution = 3.81
  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=   0.002 sd=   0.029
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: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    4194      2.51       5
     N    1075      2.21       5
     O    1238      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6539
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 598, 4724
          Classifications: {'peptide': 598}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 32, 'TRANS': 565}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 26
    Chain: "B"
      Number of atoms: 1815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1815
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 8, 'TRANS': 226}
          Chain breaks: 1
  Time building chain proxies: 1.61, per 1000 atoms: 0.25
  Number of scatterers: 6539
  At special positions: 0
  Unit cell: (71.288, 90.44, 131.936, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1238      8.00
     N    1075      7.00
     C    4194      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 160 " - pdb=" SG  CYS B 234 " distance=2.03

  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: 0.49
  Conformation dependent library (CDL) restraints added in 343.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 19 sheets defined
      3.5% alpha, 20.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 301
    Processing helix  chain 'A' and resid 406 through 411
    Processing helix  chain 'A' and resid 502 through 506
      removed outlier: 3.687A  pdb=" N   GLN A 506 " --> pdb=" O   VAL A 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 4.348A  pdb=" N   TYR B  32 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 229
      removed outlier: 3.700A  pdb=" N   THR B 229 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29
      removed outlier: 3.724A  pdb=" N   THR A  63 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 267 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49
      removed outlier: 3.923A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.688A  pdb=" N   GLY A 107 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 95
      removed outlier: 5.911A  pdb=" N   SER A 203 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 120
      removed outlier: 3.611A  pdb=" N   ILE A 128 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314
      removed outlier: 3.528A  pdb=" N   ALA A 609 " --> pdb=" O   ILE A 598 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A 610 " --> pdb=" O   ILE A 651 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A 651 " --> pdb=" O   VAL A 610 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR A 612 " --> pdb=" O   CYS A 649 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   CYS A 649 " --> pdb=" O   TYR A 612 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLY A 648 " --> pdb=" O   THR A 645 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   THR A 645 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   LEU A 650 " --> pdb=" O   PHE A 643 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   PHE A 643 " --> pdb=" O   LEU A 650 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326
    Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 357
      removed outlier: 3.883A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ASP A 398 " --> pdb=" O   VAL A 512 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   VAL A 512 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362
      removed outlier: 7.371A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB2, first strand: chain 'A' and resid 655 through 660
      removed outlier: 6.527A  pdb=" N   ASN A 658 " --> pdb=" O   THR A 696 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 664 through 667
      removed outlier: 6.862A  pdb=" N   ILE A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 674 through 675
    Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 7
    Processing sheet with id=AB6, first strand: chain 'B' and resid 17 through 18
      removed outlier: 3.662A  pdb=" N   MET B  82 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 56 through 59
      removed outlier: 3.800A  pdb=" N   ARG B  56 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   TRP B  36 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   SER B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   MET B  34 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL B  37 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TYR B  94 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   TYR B  93 " --> pdb=" O   THR B 112 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 112 " --> pdb=" O   TYR B  93 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 149 through 150
    Processing sheet with id=AB9, first strand: chain 'B' and resid 157 through 161
      removed outlier: 3.529A  pdb=" N   THR B 207 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 173
      removed outlier: 3.631A  pdb=" N   ALA B 235 " --> pdb=" O   SER B 173 " (cutoff:3.500A)

    112 hydrogen bonds defined for protein.
    264 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2080
        1.35 -     1.46: 1704
        1.46 -     1.58: 2878
        1.58 -     1.70: 0
        1.70 -     1.81: 41
  Bond restraints: 6703
  Sorted by residual:
  bond pdb=" C   GLU A 212 "
       pdb=" N   PRO A 213 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 7.92e-01
  bond pdb=" C   ILE A 664 "
       pdb=" O   ILE A 664 "
    ideal  model  delta    sigma   weight residual
    1.240  1.231  0.009 1.26e-02 6.30e+03 5.02e-01
  bond pdb=" C   GLN A 173 "
       pdb=" N   PRO A 174 "
    ideal  model  delta    sigma   weight residual
    1.330  1.338 -0.008 1.19e-02 7.06e+03 4.31e-01
  bond pdb=" CB  PRO A 330 "
       pdb=" CG  PRO A 330 "
    ideal  model  delta    sigma   weight residual
    1.492  1.523 -0.031 5.00e-02 4.00e+02 3.96e-01
  bond pdb=" N   ASP B  26 "
       pdb=" CA  ASP B  26 "
    ideal  model  delta    sigma   weight residual
    1.460  1.469 -0.009 1.54e-02 4.22e+03 3.31e-01
  ... (remaining 6698 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 8836
        1.03 -     2.06: 207
        2.06 -     3.09: 64
        3.09 -     4.12: 9
        4.12 -     5.15: 2
  Bond angle restraints: 9118
  Sorted by residual:
  angle pdb=" N   ASP A  80 "
        pdb=" CA  ASP A  80 "
        pdb=" C   ASP A  80 "
      ideal   model   delta    sigma   weight residual
     114.56  111.04    3.52 1.27e+00 6.20e-01 7.68e+00
  angle pdb=" CA  ASP A  80 "
        pdb=" C   ASP A  80 "
        pdb=" N   ASN A  81 "
      ideal   model   delta    sigma   weight residual
     119.26  116.87    2.39 1.14e+00 7.69e-01 4.40e+00
  angle pdb=" CA  ASP A  80 "
        pdb=" C   ASP A  80 "
        pdb=" O   ASP A  80 "
      ideal   model   delta    sigma   weight residual
     118.55  120.50   -1.95 1.14e+00 7.69e-01 2.94e+00
  angle pdb=" C   SER B  25 "
        pdb=" N   ASP B  26 "
        pdb=" CA  ASP B  26 "
      ideal   model   delta    sigma   weight residual
     122.46  124.71   -2.25 1.41e+00 5.03e-01 2.55e+00
  angle pdb=" C   PHE A 559 "
        pdb=" N   LEU A 560 "
        pdb=" CA  LEU A 560 "
      ideal   model   delta    sigma   weight residual
     121.80  125.69   -3.89 2.44e+00 1.68e-01 2.54e+00
  ... (remaining 9113 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 3736
       16.03 -    32.05: 166
       32.05 -    48.08: 35
       48.08 -    64.10: 6
       64.10 -    80.13: 1
  Dihedral angle restraints: 3944
    sinusoidal: 1525
      harmonic: 2419
  Sorted by residual:
  dihedral pdb=" N   LYS A 424 "
           pdb=" CA  LYS A 424 "
           pdb=" CB  LYS A 424 "
           pdb=" CG  LYS A 424 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.01  -59.99     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   LEU A 390 "
           pdb=" CA  LEU A 390 "
           pdb=" CB  LEU A 390 "
           pdb=" CG  LEU A 390 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.77   56.77     3      1.50e+01 4.44e-03 9.41e+00
  dihedral pdb=" N   PHE A 329 "
           pdb=" CA  PHE A 329 "
           pdb=" CB  PHE A 329 "
           pdb=" CG  PHE A 329 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.13  -54.87     3      1.50e+01 4.44e-03 9.31e+00
  ... (remaining 3941 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 572
       0.025 -    0.050: 259
       0.050 -    0.076: 83
       0.076 -    0.101: 60
       0.101 -    0.126: 29
  Chirality restraints: 1003
  Sorted by residual:
  chirality pdb=" CA  ILE A 101 "
            pdb=" N   ILE A 101 "
            pdb=" C   ILE A 101 "
            pdb=" CB  ILE A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.96e-01
  chirality pdb=" CA  ILE A 584 "
            pdb=" N   ILE A 584 "
            pdb=" C   ILE A 584 "
            pdb=" CB  ILE A 584 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  ILE A 235 "
            pdb=" N   ILE A 235 "
            pdb=" C   ILE A 235 "
            pdb=" CB  ILE A 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 1000 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 173 "    0.037 5.00e-02 4.00e+02   5.59e-02 5.00e+00
        pdb=" N   PRO A 174 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 174 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 174 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 321 "   -0.031 5.00e-02 4.00e+02   4.78e-02 3.65e+00
        pdb=" N   PRO A 322 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 336 "    0.019 5.00e-02 4.00e+02   2.83e-02 1.28e+00
        pdb=" N   PRO A 337 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 337 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 337 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1589
        2.79 -     3.32: 5895
        3.32 -     3.84: 10478
        3.84 -     4.37: 11962
        4.37 -     4.90: 20458
  Nonbonded interactions: 50382
  Sorted by model distance:
  nonbonded pdb=" O   ASP B  89 "
            pdb=" OH  TYR B  93 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   VAL A 130 "
            pdb=" OG1 THR A 167 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   THR A 393 "
            pdb=" OG1 THR A 523 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OG1 THR A 470 "
            pdb=" OG  SER B  54 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   GLU A 661 "
            pdb=" OH  TYR A 695 "
     model   vdw
     2.295 3.040
  ... (remaining 50377 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:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.900
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6485
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      :  0.001   0.031   6714  Z= 0.080
  Angle     :  0.433   5.155   9140  Z= 0.240
  Chirality :  0.040   0.126   1003
  Planarity :  0.004   0.056   1175
  Dihedral  :  9.227  80.126   2367
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  :  7.52 %
    Favored  : 86.63 %
  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: -4.65 (0.24), residues: 815
  helix: -2.48 (1.17), residues: 14
  sheet: -2.96 (0.34), residues: 172
  loop : -3.44 (0.20), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.005   0.001   TYR B 169 
 PHE   0.005   0.001   PHE A 192 
 TRP   0.003   0.000   TRP B  99 
 HIS   0.001   0.000   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00149 ( 6703)
  covalent geometry    : angle       0.43270 ( 9118)
  SS BOND              : bond        0.00135 (   11)
  SS BOND              : angle       0.42984 (   22)
  hydrogen bonds       : bond        0.22635 (  112)
  hydrogen bonds       : angle       9.04735 (  264)

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 246
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.5984 (t80) cc_final: 0.5726 (t80)
REVERT: A   95 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7598 (tp)
REVERT: A  177 MET cc_start: 0.6113 (mmt) cc_final: 0.5835 (mmt)
REVERT: A  294 ASP cc_start: 0.7943 (p0) cc_final: 0.7652 (p0)
REVERT: A  357 ARG cc_start: 0.6937 (ttp80) cc_final: 0.6561 (ttp80)
REVERT: A  368 LEU cc_start: 0.7611 (mm) cc_final: 0.7289 (tp)
REVERT: A  387 LEU cc_start: 0.8674 (mt) cc_final: 0.8256 (tp)
REVERT: A  388 ASN cc_start: 0.7787 (m110) cc_final: 0.7457 (p0)
REVERT: A  394 ASN cc_start: 0.7343 (m-40) cc_final: 0.7116 (m-40)
REVERT: A  395 VAL cc_start: 0.7655 (m) cc_final: 0.7378 (t)
REVERT: A  408 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7476 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7679 (t0) cc_final: 0.7403 (t0)
REVERT: A  428 ASP cc_start: 0.7345 (p0) cc_final: 0.7009 (p0)
REVERT: A  452 LEU cc_start: 0.7605 (mp) cc_final: 0.7186 (tt)
REVERT: A  470 THR cc_start: 0.7394 (p) cc_final: 0.7115 (p)
REVERT: A  490 PHE cc_start: 0.8416 (t80) cc_final: 0.8200 (t80)
REVERT: A  537 LYS cc_start: 0.7724 (tppp) cc_final: 0.7186 (mmmm)
REVERT: A  562 PHE cc_start: 0.6663 (t80) cc_final: 0.5853 (t80)
REVERT: A  699 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8382 (pt)
REVERT: B   82 MET cc_start: 0.8750 (mtt) cc_final: 0.8323 (mtt)
REVERT: B   93 TYR cc_start: 0.6581 (m-80) cc_final: 0.5874 (m-80)
REVERT: B  167 PHE cc_start: 0.6732 (m-80) cc_final: 0.6529 (m-80)
REVERT: B  215 ASN cc_start: 0.8693 (m-40) cc_final: 0.8447 (t0)
REVERT: B  252 THR cc_start: 0.8471 (t) cc_final: 0.8264 (p)
  outliers start: 42
  outliers final: 14
  residues processed: 270
  average time/residue: 0.0950
  time to fit residues: 32.7066
Evaluate side-chains
  218 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 202
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  547 LYS
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue  208 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A  66 HIS
A  87 ASN
A 173 GLN
A 234 ASN
A 271 GLN
A 280 ASN
A 321 GLN
A 360 ASN
A 388 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 536 ASN
A 563 GLN
** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   3 GLN
B  13 GLN
B  81 GLN
B 110 GLN
B 141 GLN
B 212 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.171799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.138754 restraints weight = 12629.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.144766 restraints weight = 7417.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.148937 restraints weight = 4963.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.151930 restraints weight = 3637.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.154078 restraints weight = 2837.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   6714  Z= 0.202
  Angle     :  0.667   7.357   9140  Z= 0.344
  Chirality :  0.046   0.256   1003
  Planarity :  0.005   0.053   1175
  Dihedral  :  6.840  82.143    950
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.66 %
    Favored  : 88.34 %
  Rotamer:
    Outliers :  7.10 %
    Allowed  : 12.95 %
    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: -4.08 (0.26), residues: 815
  helix: -2.53 (1.21), residues: 16
  sheet: -2.90 (0.35), residues: 185
  loop : -2.87 (0.22), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  86 
 TYR   0.011   0.001   TYR A 612 
 PHE   0.037   0.002   PHE A 306 
 TRP   0.029   0.002   TRP B 174 
 HIS   0.019   0.003   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 6703)
  covalent geometry    : angle       0.66340 ( 9118)
  SS BOND              : bond        0.00830 (   11)
  SS BOND              : angle       1.53115 (   22)
  hydrogen bonds       : bond        0.03883 (  112)
  hydrogen bonds       : angle       7.62843 (  264)

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 226
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 VAL cc_start: 0.8411 (p) cc_final: 0.7765 (m)
REVERT: A   86 PHE cc_start: 0.8529 (t80) cc_final: 0.8072 (t80)
REVERT: A  177 MET cc_start: 0.6266 (mmt) cc_final: 0.5946 (mmt)
REVERT: A  204 LYS cc_start: 0.8252 (tttp) cc_final: 0.7915 (tttp)
REVERT: A  265 TYR cc_start: 0.6629 (m-80) cc_final: 0.6239 (m-80)
REVERT: A  319 ARG cc_start: 0.7934 (ptp90) cc_final: 0.7665 (tpt170)
REVERT: A  340 GLU cc_start: 0.7732 (mp0) cc_final: 0.7493 (mp0)
REVERT: A  357 ARG cc_start: 0.7322 (ttp80) cc_final: 0.6877 (ttp80)
REVERT: A  359 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.7920 (t)
REVERT: A  368 LEU cc_start: 0.8344 (mm) cc_final: 0.7832 (tt)
REVERT: A  387 LEU cc_start: 0.8655 (mt) cc_final: 0.8335 (tp)
REVERT: A  395 VAL cc_start: 0.7895 (m) cc_final: 0.7672 (m)
REVERT: A  408 ARG cc_start: 0.8061 (ttp-170) cc_final: 0.7654 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7893 (t0) cc_final: 0.7515 (t0)
REVERT: A  424 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7821 (tmtm)
REVERT: A  442 ASP cc_start: 0.8176 (p0) cc_final: 0.7918 (p0)
REVERT: A  452 LEU cc_start: 0.7791 (mp) cc_final: 0.7231 (tt)
REVERT: A  501 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7390 (t80)
REVERT: A  528 LYS cc_start: 0.7785 (mttm) cc_final: 0.7298 (mttp)
REVERT: A  537 LYS cc_start: 0.7905 (tppp) cc_final: 0.7511 (mmmm)
REVERT: A  562 PHE cc_start: 0.6858 (t80) cc_final: 0.6356 (t80)
REVERT: A  588 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8681 (p)
REVERT: A  598 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8168 (tp)
REVERT: B   45 PRO cc_start: 0.8732 (Cg_endo) cc_final: 0.8477 (Cg_exo)
REVERT: B   64 LYS cc_start: 0.8348 (tptt) cc_final: 0.8060 (tptt)
REVERT: B   82 MET cc_start: 0.8512 (mtt) cc_final: 0.8311 (mtt)
REVERT: B   93 TYR cc_start: 0.6894 (m-80) cc_final: 0.6350 (m-80)
REVERT: B   97 SER cc_start: 0.7930 (OUTLIER) cc_final: 0.7612 (p)
REVERT: B  189 ILE cc_start: 0.8797 (mm) cc_final: 0.8451 (mm)
REVERT: B  252 THR cc_start: 0.8359 (t) cc_final: 0.8108 (m)
  outliers start: 51
  outliers final: 25
  residues processed: 253
  average time/residue: 0.1023
  time to fit residues: 32.7115
Evaluate side-chains
  241 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 210
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  170 TYR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  297 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  547 LYS
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  216 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 77 optimal weight:    0.3980
   chunk 68 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0010
   overall best weight:    0.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.166429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.134158 restraints weight = 12571.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.139937 restraints weight = 7478.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.144013 restraints weight = 5050.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.146862 restraints weight = 3717.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.148848 restraints weight = 2925.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.4152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6714  Z= 0.143
  Angle     :  0.661   8.461   9140  Z= 0.336
  Chirality :  0.045   0.161   1003
  Planarity :  0.005   0.077   1175
  Dihedral  :  6.606  80.642    940
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.18 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 19.92 %
    Favored  : 75.35 %
  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: -3.81 (0.27), residues: 815
  helix: -2.19 (1.25), residues: 17
  sheet: -2.54 (0.38), residues: 170
  loop : -2.76 (0.22), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  38 
 TYR   0.013   0.001   TYR B 107 
 PHE   0.027   0.002   PHE A 275 
 TRP   0.040   0.002   TRP B 174 
 HIS   0.016   0.003   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6703)
  covalent geometry    : angle       0.65840 ( 9118)
  SS BOND              : bond        0.00691 (   11)
  SS BOND              : angle       1.39982 (   22)
  hydrogen bonds       : bond        0.03122 (  112)
  hydrogen bonds       : angle       7.26616 (  264)

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 214
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7756 (tp40) cc_final: 0.7413 (tp40)
REVERT: A   67 VAL cc_start: 0.8371 (p) cc_final: 0.7823 (m)
REVERT: A   86 PHE cc_start: 0.8523 (t80) cc_final: 0.8233 (t80)
REVERT: A  177 MET cc_start: 0.6229 (mmt) cc_final: 0.5909 (mmt)
REVERT: A  224 GLU cc_start: 0.7372 (pm20) cc_final: 0.6578 (pm20)
REVERT: A  265 TYR cc_start: 0.6702 (m-80) cc_final: 0.6251 (m-80)
REVERT: A  313 TYR cc_start: 0.6047 (m-80) cc_final: 0.5543 (m-80)
REVERT: A  319 ARG cc_start: 0.7905 (ptp90) cc_final: 0.7645 (tpt170)
REVERT: A  340 GLU cc_start: 0.7808 (mp0) cc_final: 0.7533 (mp0)
REVERT: A  357 ARG cc_start: 0.7280 (ttp80) cc_final: 0.6857 (ttp80)
REVERT: A  368 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8033 (tt)
REVERT: A  386 LYS cc_start: 0.8339 (ttpp) cc_final: 0.8138 (ptmm)
REVERT: A  387 LEU cc_start: 0.8670 (mt) cc_final: 0.8379 (tp)
REVERT: A  401 VAL cc_start: 0.8046 (t) cc_final: 0.7658 (m)
REVERT: A  408 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7619 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7831 (t0) cc_final: 0.7472 (t0)
REVERT: A  418 ILE cc_start: 0.8200 (pp) cc_final: 0.7976 (pp)
REVERT: A  422 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7968 (t0)
REVERT: A  424 LYS cc_start: 0.8144 (tmtm) cc_final: 0.7812 (tmtm)
REVERT: A  442 ASP cc_start: 0.8228 (p0) cc_final: 0.7822 (p0)
REVERT: A  452 LEU cc_start: 0.7575 (mp) cc_final: 0.7076 (tt)
REVERT: A  501 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7409 (t80)
REVERT: A  588 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8620 (p)
REVERT: B   64 LYS cc_start: 0.8147 (tptt) cc_final: 0.7809 (tptt)
REVERT: B  107 TYR cc_start: 0.6226 (t80) cc_final: 0.5404 (t80)
REVERT: B  143 VAL cc_start: 0.8905 (m) cc_final: 0.8644 (p)
REVERT: B  158 LEU cc_start: 0.7837 (mm) cc_final: 0.7067 (mt)
REVERT: B  189 ILE cc_start: 0.8733 (mm) cc_final: 0.8432 (mm)
  outliers start: 34
  outliers final: 20
  residues processed: 234
  average time/residue: 0.1017
  time to fit residues: 30.1145
Evaluate side-chains
  220 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 196
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  206 PHE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  231 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0060
   chunk 38 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 14 optimal weight:    0.0980
   overall best weight:    0.2596

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

Flipped N/Q/H residues before XYZ refinement:
A 271 GLN
A 321 GLN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 540 ASN
A 580 GLN
A 607 GLN
A 690 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.169950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.137718 restraints weight = 12527.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.143592 restraints weight = 7366.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.147613 restraints weight = 4931.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.150416 restraints weight = 3620.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.152476 restraints weight = 2848.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.4140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6650
moved from start:          0.4491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6714  Z= 0.112
  Angle     :  0.658   9.763   9140  Z= 0.329
  Chirality :  0.045   0.181   1003
  Planarity :  0.005   0.060   1175
  Dihedral  :  6.427  80.888    934
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 20.89 %
    Favored  : 74.37 %
  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: -3.61 (0.27), residues: 815
  helix: -0.99 (1.71), residues: 10
  sheet: -2.55 (0.35), residues: 194
  loop : -2.56 (0.23), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  38 
 TYR   0.015   0.001   TYR B  52 
 PHE   0.035   0.002   PHE A 275 
 TRP   0.040   0.001   TRP B 174 
 HIS   0.009   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6703)
  covalent geometry    : angle       0.65706 ( 9118)
  SS BOND              : bond        0.00446 (   11)
  SS BOND              : angle       0.92849 (   22)
  hydrogen bonds       : bond        0.02983 (  112)
  hydrogen bonds       : angle       6.84462 (  264)

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 203
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7522 (tp40) cc_final: 0.7207 (tp40)
REVERT: A   86 PHE cc_start: 0.8397 (t80) cc_final: 0.8105 (t80)
REVERT: A   92 PHE cc_start: 0.6418 (t80) cc_final: 0.6142 (t80)
REVERT: A  177 MET cc_start: 0.6270 (mmt) cc_final: 0.5960 (mmt)
REVERT: A  204 LYS cc_start: 0.8272 (tppt) cc_final: 0.8024 (tppt)
REVERT: A  308 VAL cc_start: 0.8364 (p) cc_final: 0.7990 (t)
REVERT: A  313 TYR cc_start: 0.5785 (m-80) cc_final: 0.5275 (m-80)
REVERT: A  319 ARG cc_start: 0.7838 (ptp90) cc_final: 0.7578 (tpt170)
REVERT: A  328 ARG cc_start: 0.7034 (mmm-85) cc_final: 0.6058 (mmm-85)
REVERT: A  340 GLU cc_start: 0.7941 (mp0) cc_final: 0.7718 (mp0)
REVERT: A  355 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.6686 (ttm-80)
REVERT: A  357 ARG cc_start: 0.7202 (ttp80) cc_final: 0.6820 (ttp80)
REVERT: A  359 SER cc_start: 0.8108 (m) cc_final: 0.7644 (t)
REVERT: A  368 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8102 (tp)
REVERT: A  401 VAL cc_start: 0.7952 (t) cc_final: 0.7549 (m)
REVERT: A  408 ARG cc_start: 0.7919 (ttp-170) cc_final: 0.7515 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7702 (t0) cc_final: 0.7483 (t0)
REVERT: A  424 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7485 (tmtm)
REVERT: A  452 LEU cc_start: 0.7423 (mp) cc_final: 0.6862 (tt)
REVERT: A  501 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7426 (t80)
REVERT: A  547 LYS cc_start: 0.7446 (mmmt) cc_final: 0.6877 (mmmt)
REVERT: A  578 ASP cc_start: 0.8139 (t70) cc_final: 0.7666 (t0)
REVERT: B   64 LYS cc_start: 0.8188 (tptt) cc_final: 0.7853 (tptt)
REVERT: B  143 VAL cc_start: 0.8600 (m) cc_final: 0.8320 (p)
REVERT: B  189 ILE cc_start: 0.8681 (mm) cc_final: 0.8349 (mm)
REVERT: B  197 TYR cc_start: 0.6902 (m-80) cc_final: 0.6695 (m-80)
REVERT: B  215 ASN cc_start: 0.9140 (t0) cc_final: 0.8930 (t0)
REVERT: B  228 ASP cc_start: 0.8141 (m-30) cc_final: 0.7921 (m-30)
REVERT: B  234 CYS cc_start: 0.4976 (p) cc_final: 0.4344 (p)
  outliers start: 34
  outliers final: 25
  residues processed: 226
  average time/residue: 0.1025
  time to fit residues: 29.2765
Evaluate side-chains
  218 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 190
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  690 GLN
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  206 PHE
Chi-restraints excluded: chain B residue  208 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 79 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 10 optimal weight:   10.0000
   chunk 22 optimal weight:    0.3980
   chunk 19 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 321 GLN
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 519 HIS
A 564 GLN
A 580 GLN
A 607 GLN
A 690 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.167997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.135063 restraints weight = 12619.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.140796 restraints weight = 7422.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.144736 restraints weight = 4982.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.147517 restraints weight = 3674.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.149528 restraints weight = 2905.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6714  Z= 0.125
  Angle     :  0.660   8.560   9140  Z= 0.333
  Chirality :  0.046   0.156   1003
  Planarity :  0.005   0.056   1175
  Dihedral  :  6.547  79.626    934
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.17 %
    Favored  : 88.83 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 20.89 %
    Favored  : 73.82 %
  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: -3.50 (0.27), residues: 815
  helix: -0.99 (1.49), residues: 9
  sheet: -2.47 (0.36), residues: 188
  loop : -2.49 (0.23), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  38 
 TYR   0.011   0.001   TYR B 107 
 PHE   0.022   0.001   PHE A 275 
 TRP   0.060   0.002   TRP B 174 
 HIS   0.009   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6703)
  covalent geometry    : angle       0.65901 ( 9118)
  SS BOND              : bond        0.00455 (   11)
  SS BOND              : angle       1.07337 (   22)
  hydrogen bonds       : bond        0.02986 (  112)
  hydrogen bonds       : angle       6.88980 (  264)

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 200
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7326 (tp40) cc_final: 0.7099 (tp-100)
REVERT: A   54 LEU cc_start: 0.8250 (mt) cc_final: 0.7540 (mm)
REVERT: A   55 PHE cc_start: 0.7496 (m-80) cc_final: 0.7000 (m-10)
REVERT: A   86 PHE cc_start: 0.8391 (t80) cc_final: 0.8133 (t80)
REVERT: A  177 MET cc_start: 0.6369 (mmt) cc_final: 0.6035 (mmt)
REVERT: A  204 LYS cc_start: 0.8324 (tppt) cc_final: 0.8057 (tppt)
REVERT: A  224 GLU cc_start: 0.7111 (pm20) cc_final: 0.6672 (pm20)
REVERT: A  313 TYR cc_start: 0.6077 (m-80) cc_final: 0.5457 (m-80)
REVERT: A  328 ARG cc_start: 0.7206 (mmm-85) cc_final: 0.6247 (mmm-85)
REVERT: A  340 GLU cc_start: 0.8063 (mp0) cc_final: 0.7744 (mp0)
REVERT: A  357 ARG cc_start: 0.7347 (ttp80) cc_final: 0.6958 (ttp80)
REVERT: A  359 SER cc_start: 0.8168 (m) cc_final: 0.7654 (t)
REVERT: A  387 LEU cc_start: 0.8674 (mt) cc_final: 0.8382 (mt)
REVERT: A  401 VAL cc_start: 0.8068 (t) cc_final: 0.7632 (m)
REVERT: A  408 ARG cc_start: 0.7931 (ttp-170) cc_final: 0.7528 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7864 (t0) cc_final: 0.7640 (t0)
REVERT: A  424 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7556 (tmtm)
REVERT: A  452 LEU cc_start: 0.7404 (mp) cc_final: 0.6858 (tt)
REVERT: A  501 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7495 (t80)
REVERT: A  542 ASN cc_start: 0.7878 (m-40) cc_final: 0.6959 (p0)
REVERT: A  588 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8505 (p)
REVERT: B   38 ARG cc_start: 0.7144 (ttp80) cc_final: 0.6833 (ttp80)
REVERT: B   64 LYS cc_start: 0.8204 (tptt) cc_final: 0.7843 (tptt)
REVERT: B  142 LEU cc_start: 0.8627 (mm) cc_final: 0.7777 (pt)
REVERT: B  158 LEU cc_start: 0.7729 (mm) cc_final: 0.7445 (mt)
REVERT: B  189 ILE cc_start: 0.8719 (mm) cc_final: 0.8380 (mm)
REVERT: B  215 ASN cc_start: 0.9128 (t0) cc_final: 0.8842 (t0)
  outliers start: 38
  outliers final: 26
  residues processed: 222
  average time/residue: 0.1049
  time to fit residues: 29.4244
Evaluate side-chains
  225 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 196
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  206 PHE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  231 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 80 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0570
   chunk 18 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 321 GLN
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
A 580 GLN
B   3 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.167329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.134918 restraints weight = 12811.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.140479 restraints weight = 7577.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.144337 restraints weight = 5106.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.147094 restraints weight = 3771.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.149077 restraints weight = 2984.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.5192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6714  Z= 0.129
  Angle     :  0.667   8.054   9140  Z= 0.339
  Chirality :  0.046   0.155   1003
  Planarity :  0.005   0.055   1175
  Dihedral  :  6.619  80.725    934
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.17 %
    Favored  : 88.83 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 22.84 %
    Favored  : 72.01 %
  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: -3.44 (0.27), residues: 815
  helix: -1.51 (1.47), residues: 10
  sheet: -2.30 (0.37), residues: 188
  loop : -2.48 (0.23), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  38 
 TYR   0.014   0.001   TYR B  32 
 PHE   0.030   0.002   PHE B 165 
 TRP   0.067   0.002   TRP B 174 
 HIS   0.002   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6703)
  covalent geometry    : angle       0.66468 ( 9118)
  SS BOND              : bond        0.00555 (   11)
  SS BOND              : angle       1.38270 (   22)
  hydrogen bonds       : bond        0.03129 (  112)
  hydrogen bonds       : angle       6.82653 (  264)

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 204
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.8170 (mt) cc_final: 0.7797 (mt)
REVERT: A   55 PHE cc_start: 0.7418 (m-80) cc_final: 0.6760 (m-80)
REVERT: A   86 PHE cc_start: 0.8421 (t80) cc_final: 0.8180 (t80)
REVERT: A  177 MET cc_start: 0.6346 (mmt) cc_final: 0.6030 (mmt)
REVERT: A  204 LYS cc_start: 0.8328 (tppt) cc_final: 0.8091 (tppt)
REVERT: A  224 GLU cc_start: 0.7181 (pm20) cc_final: 0.6805 (pm20)
REVERT: A  313 TYR cc_start: 0.6070 (m-80) cc_final: 0.5504 (m-80)
REVERT: A  340 GLU cc_start: 0.8109 (mp0) cc_final: 0.7788 (mp0)
REVERT: A  357 ARG cc_start: 0.7420 (ttp80) cc_final: 0.6987 (ttp80)
REVERT: A  359 SER cc_start: 0.8149 (m) cc_final: 0.7685 (t)
REVERT: A  387 LEU cc_start: 0.8661 (mt) cc_final: 0.8382 (mt)
REVERT: A  401 VAL cc_start: 0.8034 (t) cc_final: 0.7618 (m)
REVERT: A  408 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7547 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7897 (t0) cc_final: 0.7526 (t0)
REVERT: A  424 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7628 (tmtm)
REVERT: A  452 LEU cc_start: 0.7379 (mp) cc_final: 0.6821 (tt)
REVERT: A  501 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7534 (t80)
REVERT: A  547 LYS cc_start: 0.7317 (mmmt) cc_final: 0.6477 (mmmt)
REVERT: A  591 SER cc_start: 0.7649 (m) cc_final: 0.7298 (p)
REVERT: B   29 PHE cc_start: 0.8159 (m-80) cc_final: 0.7560 (m-80)
REVERT: B   38 ARG cc_start: 0.7219 (ttp80) cc_final: 0.6859 (ttp80)
REVERT: B   64 LYS cc_start: 0.8224 (tptt) cc_final: 0.7865 (tptt)
REVERT: B  142 LEU cc_start: 0.8552 (mm) cc_final: 0.7546 (tp)
REVERT: B  189 ILE cc_start: 0.8633 (mm) cc_final: 0.8338 (mm)
REVERT: B  215 ASN cc_start: 0.9151 (t0) cc_final: 0.8877 (t0)
  outliers start: 37
  outliers final: 30
  residues processed: 225
  average time/residue: 0.0888
  time to fit residues: 25.6301
Evaluate side-chains
  221 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 189
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  234 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 78 optimal weight:    7.9990
   chunk 79 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0470
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 ASN
A 321 GLN
** A 409 GLN ** 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 = 0.4309 r_free = 0.4309 target = 0.166087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.133624 restraints weight = 12649.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.139212 restraints weight = 7434.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.143084 restraints weight = 4987.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.145791 restraints weight = 3672.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.147743 restraints weight = 2907.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.4093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.5443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6714  Z= 0.132
  Angle     :  0.702   9.498   9140  Z= 0.357
  Chirality :  0.047   0.220   1003
  Planarity :  0.005   0.055   1175
  Dihedral  :  6.808  80.186    934
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.29 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 23.26 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -3.34 (0.27), residues: 815
  helix: -1.86 (1.32), residues: 17
  sheet: -2.10 (0.38), residues: 178
  loop : -2.46 (0.23), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 205 
 TYR   0.014   0.001   TYR B  32 
 PHE   0.021   0.002   PHE A  55 
 TRP   0.071   0.002   TRP B 174 
 HIS   0.002   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6703)
  covalent geometry    : angle       0.69174 ( 9118)
  SS BOND              : bond        0.00476 (   11)
  SS BOND              : angle       2.56240 (   22)
  hydrogen bonds       : bond        0.03311 (  112)
  hydrogen bonds       : angle       6.71737 (  264)

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 192
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.8103 (mt) cc_final: 0.7784 (mt)
REVERT: A   55 PHE cc_start: 0.7321 (m-80) cc_final: 0.6618 (m-80)
REVERT: A  170 TYR cc_start: 0.8683 (t80) cc_final: 0.8342 (t80)
REVERT: A  177 MET cc_start: 0.6386 (mmt) cc_final: 0.6068 (mmt)
REVERT: A  224 GLU cc_start: 0.7028 (pm20) cc_final: 0.6752 (pm20)
REVERT: A  313 TYR cc_start: 0.5964 (m-80) cc_final: 0.5388 (m-80)
REVERT: A  328 ARG cc_start: 0.7062 (mmm-85) cc_final: 0.6046 (mmm-85)
REVERT: A  340 GLU cc_start: 0.8116 (mp0) cc_final: 0.7815 (mp0)
REVERT: A  357 ARG cc_start: 0.7369 (ttp80) cc_final: 0.6991 (ttp80)
REVERT: A  359 SER cc_start: 0.8252 (m) cc_final: 0.7853 (t)
REVERT: A  387 LEU cc_start: 0.8614 (mt) cc_final: 0.8342 (mt)
REVERT: A  388 ASN cc_start: 0.8250 (p0) cc_final: 0.7879 (t0)
REVERT: A  401 VAL cc_start: 0.8007 (t) cc_final: 0.7600 (m)
REVERT: A  408 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.7540 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7836 (t0) cc_final: 0.7486 (t0)
REVERT: A  452 LEU cc_start: 0.7402 (mp) cc_final: 0.6858 (tt)
REVERT: A  501 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7474 (t80)
REVERT: A  542 ASN cc_start: 0.7828 (m-40) cc_final: 0.6728 (p0)
REVERT: A  578 ASP cc_start: 0.8136 (t0) cc_final: 0.7785 (t0)
REVERT: A  591 SER cc_start: 0.7645 (m) cc_final: 0.7246 (p)
REVERT: B   29 PHE cc_start: 0.8135 (m-80) cc_final: 0.7528 (m-80)
REVERT: B   38 ARG cc_start: 0.7207 (ttp80) cc_final: 0.6840 (ttp80)
REVERT: B   64 LYS cc_start: 0.8242 (tptt) cc_final: 0.7886 (tptt)
REVERT: B  142 LEU cc_start: 0.8556 (mm) cc_final: 0.7661 (tp)
REVERT: B  189 ILE cc_start: 0.8617 (mm) cc_final: 0.8352 (mt)
  outliers start: 37
  outliers final: 31
  residues processed: 213
  average time/residue: 0.0896
  time to fit residues: 24.3111
Evaluate side-chains
  216 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  234 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 250 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.156705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.125753 restraints weight = 12705.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.131097 restraints weight = 7370.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.134737 restraints weight = 4905.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.137327 restraints weight = 3598.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.139163 restraints weight = 2837.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.6356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082   6714  Z= 0.281
  Angle     :  0.855  10.927   9140  Z= 0.444
  Chirality :  0.051   0.246   1003
  Planarity :  0.006   0.067   1175
  Dihedral  :  7.618  83.173    934
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 24.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.36 %
    Favored  : 85.64 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 23.54 %
    Favored  : 70.06 %
  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: -3.56 (0.27), residues: 815
  helix: -1.97 (1.07), residues: 16
  sheet: -2.70 (0.37), residues: 169
  loop : -2.47 (0.23), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 346 
 TYR   0.018   0.002   TYR B  32 
 PHE   0.043   0.003   PHE A  55 
 TRP   0.099   0.005   TRP B 174 
 HIS   0.018   0.004   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 ( 6703)
  covalent geometry    : angle       0.84077 ( 9118)
  SS BOND              : bond        0.00821 (   11)
  SS BOND              : angle       3.24322 (   22)
  hydrogen bonds       : bond        0.04458 (  112)
  hydrogen bonds       : angle       7.77148 (  264)

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 220
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TYR cc_start: 0.8267 (m-80) cc_final: 0.7948 (m-80)
REVERT: A   54 LEU cc_start: 0.8304 (mt) cc_final: 0.8094 (mt)
REVERT: A   55 PHE cc_start: 0.7523 (m-80) cc_final: 0.6826 (m-80)
REVERT: A   83 VAL cc_start: 0.8407 (t) cc_final: 0.8085 (p)
REVERT: A   86 PHE cc_start: 0.8901 (t80) cc_final: 0.8506 (t80)
REVERT: A  177 MET cc_start: 0.6815 (mmt) cc_final: 0.6487 (mmt)
REVERT: A  224 GLU cc_start: 0.7258 (pm20) cc_final: 0.6977 (pm20)
REVERT: A  337 PRO cc_start: 0.8524 (Cg_exo) cc_final: 0.8287 (Cg_endo)
REVERT: A  340 GLU cc_start: 0.8184 (mp0) cc_final: 0.7803 (mp0)
REVERT: A  343 ASN cc_start: 0.8215 (t0) cc_final: 0.7778 (p0)
REVERT: A  346 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.6856 (ppt170)
REVERT: A  354 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7993 (p0)
REVERT: A  377 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.6483 (t80)
REVERT: A  388 ASN cc_start: 0.8296 (p0) cc_final: 0.7984 (t0)
REVERT: A  401 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7603 (m)
REVERT: A  402 ILE cc_start: 0.7738 (pp) cc_final: 0.7507 (pp)
REVERT: A  406 GLU cc_start: 0.7440 (pt0) cc_final: 0.7070 (pt0)
REVERT: A  408 ARG cc_start: 0.8046 (ttp-170) cc_final: 0.7744 (ttp-170)
REVERT: A  417 ASN cc_start: 0.8193 (t0) cc_final: 0.7829 (t0)
REVERT: A  424 LYS cc_start: 0.8281 (tmtm) cc_final: 0.7902 (tptp)
REVERT: A  442 ASP cc_start: 0.8146 (p0) cc_final: 0.7815 (p0)
REVERT: A  452 LEU cc_start: 0.7786 (mp) cc_final: 0.7289 (tt)
REVERT: A  501 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7544 (t80)
REVERT: A  519 HIS cc_start: 0.7103 (m90) cc_final: 0.6689 (m90)
REVERT: A  542 ASN cc_start: 0.7970 (m-40) cc_final: 0.6873 (p0)
REVERT: A  591 SER cc_start: 0.8024 (m) cc_final: 0.7686 (p)
REVERT: A  659 SER cc_start: 0.7833 (m) cc_final: 0.7443 (t)
REVERT: B   29 PHE cc_start: 0.8169 (m-80) cc_final: 0.7548 (m-80)
REVERT: B   38 ARG cc_start: 0.7345 (ttp80) cc_final: 0.6951 (ttp80)
REVERT: B   64 LYS cc_start: 0.8389 (tptt) cc_final: 0.8020 (tptt)
REVERT: B  142 LEU cc_start: 0.8630 (mm) cc_final: 0.7619 (tp)
REVERT: B  189 ILE cc_start: 0.8708 (mm) cc_final: 0.8456 (mt)
REVERT: B  192 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7951 (tp)
REVERT: B  237 ARG cc_start: 0.6648 (ptt-90) cc_final: 0.6330 (ptt-90)
  outliers start: 46
  outliers final: 31
  residues processed: 243
  average time/residue: 0.0791
  time to fit residues: 24.6875
Evaluate side-chains
  248 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 211
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   32 TYR
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  234 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 271 GLN
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.161350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.129738 restraints weight = 12662.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.135284 restraints weight = 7299.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.139106 restraints weight = 4842.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.141903 restraints weight = 3544.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.143826 restraints weight = 2777.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6810
moved from start:          0.6432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6714  Z= 0.159
  Angle     :  0.805   9.174   9140  Z= 0.411
  Chirality :  0.049   0.217   1003
  Planarity :  0.005   0.054   1175
  Dihedral  :  7.364  82.272    934
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.52 %
    Favored  : 87.48 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 26.32 %
    Favored  : 68.11 %
  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: -3.34 (0.28), residues: 815
  helix: -1.65 (1.16), residues: 16
  sheet: -2.26 (0.36), residues: 205
  loop : -2.38 (0.24), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 357 
 TYR   0.018   0.001   TYR B 243 
 PHE   0.024   0.002   PHE A  55 
 TRP   0.081   0.003   TRP B 174 
 HIS   0.011   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6703)
  covalent geometry    : angle       0.79600 ( 9118)
  SS BOND              : bond        0.00446 (   11)
  SS BOND              : angle       2.56062 (   22)
  hydrogen bonds       : bond        0.03451 (  112)
  hydrogen bonds       : angle       7.13274 (  264)

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 210
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.8152 (mt) cc_final: 0.7935 (mt)
REVERT: A   55 PHE cc_start: 0.7183 (m-80) cc_final: 0.6403 (m-80)
REVERT: A   86 PHE cc_start: 0.8747 (t80) cc_final: 0.8367 (t80)
REVERT: A  177 MET cc_start: 0.6916 (mmt) cc_final: 0.6579 (mmt)
REVERT: A  224 GLU cc_start: 0.7219 (pm20) cc_final: 0.6934 (pm20)
REVERT: A  313 TYR cc_start: 0.6478 (m-80) cc_final: 0.5809 (m-80)
REVERT: A  337 PRO cc_start: 0.8307 (Cg_exo) cc_final: 0.7752 (Cg_endo)
REVERT: A  340 GLU cc_start: 0.8251 (mp0) cc_final: 0.7734 (mp0)
REVERT: A  355 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7764 (mtp85)
REVERT: A  377 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6400 (t80)
REVERT: A  396 TYR cc_start: 0.6968 (m-80) cc_final: 0.6673 (m-10)
REVERT: A  406 GLU cc_start: 0.7321 (pt0) cc_final: 0.6908 (pt0)
REVERT: A  408 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.7601 (ttp-170)
REVERT: A  417 ASN cc_start: 0.8098 (t0) cc_final: 0.7709 (t0)
REVERT: A  424 LYS cc_start: 0.8205 (tmtm) cc_final: 0.7827 (tmtm)
REVERT: A  442 ASP cc_start: 0.8311 (p0) cc_final: 0.7959 (p0)
REVERT: A  501 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7527 (t80)
REVERT: A  542 ASN cc_start: 0.7747 (m-40) cc_final: 0.6737 (p0)
REVERT: A  562 PHE cc_start: 0.6752 (t80) cc_final: 0.6448 (t80)
REVERT: A  591 SER cc_start: 0.7817 (m) cc_final: 0.7420 (p)
REVERT: A  659 SER cc_start: 0.7790 (m) cc_final: 0.7224 (t)
REVERT: B   29 PHE cc_start: 0.8144 (m-80) cc_final: 0.7535 (m-80)
REVERT: B   64 LYS cc_start: 0.8298 (tptt) cc_final: 0.7916 (tptt)
REVERT: B  142 LEU cc_start: 0.8588 (mm) cc_final: 0.7539 (tp)
REVERT: B  172 MET cc_start: 0.6784 (mpt) cc_final: 0.6554 (mpt)
REVERT: B  189 ILE cc_start: 0.8655 (mm) cc_final: 0.8391 (mt)
REVERT: B  192 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7770 (pt)
REVERT: B  197 TYR cc_start: 0.7382 (m-80) cc_final: 0.7169 (m-80)
REVERT: B  237 ARG cc_start: 0.6628 (ptt-90) cc_final: 0.6291 (ptt-90)
  outliers start: 40
  outliers final: 30
  residues processed: 232
  average time/residue: 0.0832
  time to fit residues: 24.7875
Evaluate side-chains
  242 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 209
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  185 TRP
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  234 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0370
   chunk 19 optimal weight:    9.9990
   chunk 20 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    0.7262

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

Flipped N/Q/H residues before XYZ refinement:
A 205 HIS
A 271 GLN
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
B 177 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.163115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.131262 restraints weight = 12508.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.136770 restraints weight = 7323.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.140616 restraints weight = 4900.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.143305 restraints weight = 3599.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.145202 restraints weight = 2846.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
moved from start:          0.6573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6714  Z= 0.160
  Angle     :  0.834   9.706   9140  Z= 0.424
  Chirality :  0.049   0.250   1003
  Planarity :  0.005   0.055   1175
  Dihedral  :  7.369  81.599    934
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.25 %
    Favored  : 86.75 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 28.55 %
    Favored  : 66.57 %
  Cbeta Deviations :  0.13 %
  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: -3.23 (0.28), residues: 815
  helix: -1.93 (1.05), residues: 22
  sheet: -1.92 (0.38), residues: 195
  loop : -2.40 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 493 
 TYR   0.017   0.002   TYR A 674 
 PHE   0.037   0.002   PHE B 165 
 TRP   0.050   0.002   TRP B 174 
 HIS   0.006   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6703)
  covalent geometry    : angle       0.82635 ( 9118)
  SS BOND              : bond        0.00489 (   11)
  SS BOND              : angle       2.47652 (   22)
  hydrogen bonds       : bond        0.03421 (  112)
  hydrogen bonds       : angle       7.04726 (  264)

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 205
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.8154 (mt) cc_final: 0.7952 (mt)
REVERT: A   55 PHE cc_start: 0.7224 (m-80) cc_final: 0.6426 (m-80)
REVERT: A   84 LEU cc_start: 0.8178 (mp) cc_final: 0.7892 (mp)
REVERT: A   86 PHE cc_start: 0.8640 (t80) cc_final: 0.8287 (t80)
REVERT: A  177 MET cc_start: 0.6956 (mmt) cc_final: 0.6637 (mmt)
REVERT: A  224 GLU cc_start: 0.7116 (pm20) cc_final: 0.6895 (pm20)
REVERT: A  239 GLN cc_start: 0.5998 (tp40) cc_final: 0.5547 (mm110)
REVERT: A  313 TYR cc_start: 0.6424 (m-80) cc_final: 0.5757 (m-80)
REVERT: A  321 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7193 (mt0)
REVERT: A  328 ARG cc_start: 0.7217 (mmm-85) cc_final: 0.6443 (mmm-85)
REVERT: A  337 PRO cc_start: 0.8205 (Cg_exo) cc_final: 0.7625 (Cg_endo)
REVERT: A  340 GLU cc_start: 0.8235 (mp0) cc_final: 0.7684 (mp0)
REVERT: A  355 ARG cc_start: 0.8082 (mtp85) cc_final: 0.7813 (mtp85)
REVERT: A  357 ARG cc_start: 0.8092 (mtp-110) cc_final: 0.7825 (mtp-110)
REVERT: A  377 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.6274 (t80)
REVERT: A  388 ASN cc_start: 0.8339 (p0) cc_final: 0.7949 (t0)
REVERT: A  390 LEU cc_start: 0.8352 (tp) cc_final: 0.7946 (pp)
REVERT: A  393 THR cc_start: 0.8525 (p) cc_final: 0.8308 (p)
REVERT: A  396 TYR cc_start: 0.6977 (m-80) cc_final: 0.6395 (m-80)
REVERT: A  406 GLU cc_start: 0.7368 (pt0) cc_final: 0.6946 (pt0)
REVERT: A  408 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7603 (ttp-170)
REVERT: A  417 ASN cc_start: 0.8077 (t0) cc_final: 0.7685 (t0)
REVERT: A  424 LYS cc_start: 0.8173 (tmtm) cc_final: 0.7783 (tmtm)
REVERT: A  442 ASP cc_start: 0.8357 (p0) cc_final: 0.7985 (p0)
REVERT: A  444 LYS cc_start: 0.9099 (tptt) cc_final: 0.8893 (tptp)
REVERT: A  490 PHE cc_start: 0.8000 (t80) cc_final: 0.7796 (t80)
REVERT: A  501 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7468 (t80)
REVERT: B   29 PHE cc_start: 0.8088 (m-80) cc_final: 0.7528 (m-80)
REVERT: B   64 LYS cc_start: 0.8147 (tptt) cc_final: 0.7849 (tptt)
REVERT: B  189 ILE cc_start: 0.8582 (mm) cc_final: 0.8348 (mt)
  outliers start: 35
  outliers final: 30
  residues processed: 224
  average time/residue: 0.0939
  time to fit residues: 26.7146
Evaluate side-chains
  236 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 204
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  185 TRP
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  234 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
A 271 GLN
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 GLN
B   3 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.155263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.123668 restraints weight = 12629.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.128968 restraints weight = 7434.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.132644 restraints weight = 5010.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.135235 restraints weight = 3702.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.136980 restraints weight = 2938.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6943
moved from start:          0.7009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.096   6714  Z= 0.280
  Angle     :  0.910  10.257   9140  Z= 0.467
  Chirality :  0.053   0.278   1003
  Planarity :  0.006   0.058   1175
  Dihedral  :  7.808  82.691    934
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 25.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.71 %
    Favored  : 84.29 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 29.11 %
    Favored  : 66.02 %
  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: -3.37 (0.28), residues: 815
  helix: -2.19 (0.95), residues: 22
  sheet: -2.36 (0.37), residues: 199
  loop : -2.35 (0.24), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 273 
 TYR   0.018   0.002   TYR A  37 
 PHE   0.038   0.003   PHE A  55 
 TRP   0.072   0.004   TRP B 174 
 HIS   0.008   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 6703)
  covalent geometry    : angle       0.89873 ( 9118)
  SS BOND              : bond        0.01006 (   11)
  SS BOND              : angle       3.06401 (   22)
  hydrogen bonds       : bond        0.04237 (  112)
  hydrogen bonds       : angle       7.56526 (  264)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1384.59 seconds
wall clock time: 24 minutes 31.07 seconds (1471.07 seconds total)