Starting phenix.real_space_refine
on Wed Sep 17 08:03:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jh8_61475/09_2025/9jh8_61475.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jh8_61475/09_2025/9jh8_61475.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jh8_61475/09_2025/9jh8_61475.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jh8_61475/09_2025/9jh8_61475.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jh8_61475/09_2025/9jh8_61475.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jh8_61475/09_2025/9jh8_61475.map"
  }
  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=   0.001 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     P      34      5.49       5
     S      20      5.16       5
     C    4244      2.51       5
     N    1118      2.21       5
     O    1337      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6754
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 745, 6036
          Classifications: {'peptide': 745}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 717}
    Chain: "C"
      Number of atoms: 359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 359
          Classifications: {'DNA': 17}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 16}
    Chain: "E"
      Number of atoms: 358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 358
          Classifications: {'DNA': 18}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 17}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.09, per 1000 atoms: 0.31
  Number of scatterers: 6754
  At special positions: 0
  Unit cell: (71.34, 82.82, 105.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      1     24.99
     S      20     16.00
     P      34     15.00
     O    1337      8.00
     N    1118      7.00
     C    4244      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 426.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1394

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 12 sheets defined
      31.9% alpha, 16.8% beta
      9 base pairs and 22 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 54
    Processing helix  chain 'A' and resid 97 through 115
      removed outlier: 3.722A  pdb=" N   TYR A 101 " --> pdb=" O   ASN A  97 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   LYS A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 193
    Processing helix  chain 'A' and resid 233 through 240
    Processing helix  chain 'A' and resid 243 through 248
    Processing helix  chain 'A' and resid 272 through 274
      No H-bonds generated for 'chain 'A' and resid 272 through 274'
    Processing helix  chain 'A' and resid 281 through 289
    Processing helix  chain 'A' and resid 289 through 301
      removed outlier: 4.519A  pdb=" N   GLN A 298 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   LEU A 299 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 364 through 369
    Processing helix  chain 'A' and resid 388 through 404
    Processing helix  chain 'A' and resid 439 through 453
      removed outlier: 3.794A  pdb=" N   TYR A 453 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 485
      removed outlier: 3.570A  pdb=" N   LEU A 485 " --> pdb=" O   ILE A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 503
    Processing helix  chain 'A' and resid 505 through 523
      removed outlier: 3.887A  pdb=" N   LEU A 509 " --> pdb=" O   ASP A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 603
      removed outlier: 3.696A  pdb=" N   LEU A 587 " --> pdb=" O   ASN A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 631
      removed outlier: 3.825A  pdb=" N   TYR A 624 " --> pdb=" O   ASP A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 712
    Processing helix  chain 'A' and resid 723 through 735
    Processing helix  chain 'A' and resid 736 through 739
      removed outlier: 4.107A  pdb=" N   ILE A 739 " --> pdb=" O   ILE A 736 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 736 through 739'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12
      removed outlier: 3.509A  pdb=" N   ASN A   9 " --> pdb=" O   ILE A 651 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE A 651 " --> pdb=" O   ASN A   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126
      removed outlier: 3.508A  pdb=" N   LEU A 134 " --> pdb=" O   ARG A 126 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   VAL A 172 " --> pdb=" O   GLY A  17 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 62
      removed outlier: 4.049A  pdb=" N   LYS A  88 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   LYS A  30 " --> pdb=" O   PHE A  86 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   PHE A  86 " --> pdb=" O   LYS A  30 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118
    Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 139
    Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 271
      removed outlier: 6.750A  pdb=" N   ILE A 259 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   VAL A 219 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   ASN A 261 " --> pdb=" O   GLU A 217 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   LEU A 214 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 359
      removed outlier: 3.960A  pdb=" N   GLY A 357 " --> pdb=" O   GLY A 354 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   LEU A 352 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 379
      removed outlier: 6.242A  pdb=" N   VAL A 378 " --> pdb=" O   GLU A 424 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 384 through 385
      removed outlier: 5.816A  pdb=" N   TYR A 384 " --> pdb=" O   TYR A 435 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 407 through 408
    Processing sheet with id=AB2, first strand: chain 'A' and resid 462 through 463
    Processing sheet with id=AB3, first strand: chain 'A' and resid 559 through 560
      removed outlier: 6.830A  pdb=" N   ILE A 637 " --> pdb=" O   SER A 693 " (cutoff:3.500A)

    233 hydrogen bonds defined for protein.
    669 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      21 hydrogen bonds
      42 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      22 stacking parallelities
  Total time for adding SS restraints: 1.36

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1479
        1.33 -     1.45: 1644
        1.45 -     1.57: 3740
        1.57 -     1.69: 65
        1.69 -     1.81: 35
  Bond restraints: 6963
  Sorted by residual:
  bond pdb=" CG1 ILE A 300 "
       pdb=" CD1 ILE A 300 "
    ideal  model  delta    sigma   weight residual
    1.513  1.392  0.121 3.90e-02 6.57e+02 9.59e+00
  bond pdb=" CG  PRO A 723 "
       pdb=" CD  PRO A 723 "
    ideal  model  delta    sigma   weight residual
    1.503  1.405  0.098 3.40e-02 8.65e+02 8.38e+00
  bond pdb=" CG1 ILE A 706 "
       pdb=" CD1 ILE A 706 "
    ideal  model  delta    sigma   weight residual
    1.513  1.408  0.105 3.90e-02 6.57e+02 7.20e+00
  bond pdb=" CG  LEU A 520 "
       pdb=" CD2 LEU A 520 "
    ideal  model  delta    sigma   weight residual
    1.521  1.438  0.083 3.30e-02 9.18e+02 6.30e+00
  bond pdb=" CB  VAL A 104 "
       pdb=" CG2 VAL A 104 "
    ideal  model  delta    sigma   weight residual
    1.521  1.442  0.079 3.30e-02 9.18e+02 5.78e+00
  ... (remaining 6958 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.50: 9376
        3.50 -     7.00: 141
        7.00 -    10.50: 16
       10.50 -    13.99: 3
       13.99 -    17.49: 1
  Bond angle restraints: 9537
  Sorted by residual:
  angle pdb=" C   TYR A 571 "
        pdb=" N   LYS A 572 "
        pdb=" CA  LYS A 572 "
      ideal   model   delta    sigma   weight residual
     121.59  139.08  -17.49 3.54e+00 7.98e-02 2.44e+01
  angle pdb=" N   LYS A  63 "
        pdb=" CA  LYS A  63 "
        pdb=" C   LYS A  63 "
      ideal   model   delta    sigma   weight residual
     110.46  103.48    6.98 1.48e+00 4.57e-01 2.22e+01
  angle pdb=" C   LYS A 631 "
        pdb=" N   ASN A 632 "
        pdb=" CA  ASN A 632 "
      ideal   model   delta    sigma   weight residual
     122.46  128.83   -6.37 1.41e+00 5.03e-01 2.04e+01
  angle pdb=" C   LYS A  63 "
        pdb=" N   ASP A  64 "
        pdb=" CA  ASP A  64 "
      ideal   model   delta    sigma   weight residual
     121.54  129.42   -7.88 1.91e+00 2.74e-01 1.70e+01
  angle pdb=" N   ILE A 523 "
        pdb=" CA  ILE A 523 "
        pdb=" C   ILE A 523 "
      ideal   model   delta    sigma   weight residual
     112.29  108.52    3.77 9.40e-01 1.13e+00 1.61e+01
  ... (remaining 9532 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.51: 3779
       23.51 -    47.02: 259
       47.02 -    70.54: 79
       70.54 -    94.05: 11
       94.05 -   117.56: 1
  Dihedral angle restraints: 4129
    sinusoidal: 1942
      harmonic: 2187
  Sorted by residual:
  dihedral pdb=" CA  GLU A 470 "
           pdb=" C   GLU A 470 "
           pdb=" N   ILE A 471 "
           pdb=" CA  ILE A 471 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.48  -32.52     0      5.00e+00 4.00e-02 4.23e+01
  dihedral pdb=" CA  ILE A 471 "
           pdb=" C   ILE A 471 "
           pdb=" N   GLU A 472 "
           pdb=" CA  GLU A 472 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.55  -30.45     0      5.00e+00 4.00e-02 3.71e+01
  dihedral pdb=" CA  ARG A 613 "
           pdb=" C   ARG A 613 "
           pdb=" N   ALA A 614 "
           pdb=" CA  ALA A 614 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.03   26.97     0      5.00e+00 4.00e-02 2.91e+01
  ... (remaining 4126 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 750
       0.066 -    0.132: 245
       0.132 -    0.199: 42
       0.199 -    0.265: 5
       0.265 -    0.331: 1
  Chirality restraints: 1043
  Sorted by residual:
  chirality pdb=" CG  LEU A 520 "
            pdb=" CB  LEU A 520 "
            pdb=" CD1 LEU A 520 "
            pdb=" CD2 LEU A 520 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.26   -0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" CG  LEU A 311 "
            pdb=" CB  LEU A 311 "
            pdb=" CD1 LEU A 311 "
            pdb=" CD2 LEU A 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CB  ILE A 712 "
            pdb=" CA  ILE A 712 "
            pdb=" CG1 ILE A 712 "
            pdb=" CG2 ILE A 712 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 1040 not shown)

  Planarity restraints: 1090
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 554 "    0.042 5.00e-02 4.00e+02   6.38e-02 6.51e+00
        pdb=" N   PRO A 555 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 555 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 555 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 623 "   -0.019 2.00e-02 2.50e+03   1.49e-02 5.54e+00
        pdb=" CG  TRP A 623 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 623 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 623 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 623 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 623 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 623 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 623 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 623 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 623 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA E  13 "   -0.027 2.00e-02 2.50e+03   1.36e-02 5.12e+00
        pdb=" N9   DA E  13 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DA E  13 "    0.006 2.00e-02 2.50e+03
        pdb=" N7   DA E  13 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DA E  13 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DA E  13 "   -0.008 2.00e-02 2.50e+03
        pdb=" N6   DA E  13 "   -0.003 2.00e-02 2.50e+03
        pdb=" N1   DA E  13 "    0.005 2.00e-02 2.50e+03
        pdb=" C2   DA E  13 "   -0.013 2.00e-02 2.50e+03
        pdb=" N3   DA E  13 "    0.019 2.00e-02 2.50e+03
        pdb=" C4   DA E  13 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1087 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 47
        2.45 -     3.07: 4294
        3.07 -     3.68: 10950
        3.68 -     4.29: 15651
        4.29 -     4.90: 25046
  Nonbonded interactions: 55988
  Sorted by model distance:
  nonbonded pdb=" OP2  DT C   1 "
            pdb="MN    MN C 801 "
     model   vdw
     1.844 2.320
  nonbonded pdb=" OP1  DA C   3 "
            pdb="MN    MN C 801 "
     model   vdw
     1.848 2.320
  nonbonded pdb=" OP1  DT C   1 "
            pdb="MN    MN C 801 "
     model   vdw
     1.918 2.320
  nonbonded pdb=" P    DT C   1 "
            pdb="MN    MN C 801 "
     model   vdw
     2.176 2.680
  nonbonded pdb=" OD1 ASN A 746 "
            pdb=" N   ARG A 747 "
     model   vdw
     2.272 3.120
  ... (remaining 55983 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.810
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
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      :  0.012   0.121   6963  Z= 0.511
  Angle     :  1.203  17.493   9537  Z= 0.655
  Chirality :  0.065   0.331   1043
  Planarity :  0.007   0.064   1090
  Dihedral  : 16.957 117.560   2735
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.40 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.89 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -3.72 (0.24), residues: 743
  helix: -2.81 (0.24), residues: 217
  sheet: -2.86 (0.40), residues: 110
  loop : -2.15 (0.26), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG A 282 
 TYR   0.031   0.004   TYR A 101 
 PHE   0.034   0.004   PHE A 540 
 TRP   0.037   0.006   TRP A 623 
 HIS   0.020   0.003   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.01179 ( 6963)
  covalent geometry    : angle       1.20300 ( 9537)
  hydrogen bonds       : bond        0.22413 (  254)
  hydrogen bonds       : angle       9.48863 (  711)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 0.264 
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
  outliers start: 1
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1183
  time to fit residues: 28.0871
Evaluate side-chains
  116 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A  97 ASN
A 240 ASN
A 325 ASN
A 368 ASN
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 ASN
A 490 GLN
A 612 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.071681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.055935 restraints weight = 32123.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.058167 restraints weight = 19147.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.059832 restraints weight = 13097.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.061023 restraints weight = 9745.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.061942 restraints weight = 7746.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6963  Z= 0.167
  Angle     :  0.763   8.454   9537  Z= 0.406
  Chirality :  0.047   0.206   1043
  Planarity :  0.005   0.032   1090
  Dihedral  : 19.984 125.853   1196
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 16.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.67 %
    Favored  : 83.38 %
  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: -2.46 (0.27), residues: 743
  helix: -0.97 (0.31), residues: 227
  sheet: -2.38 (0.41), residues: 113
  loop : -1.77 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 397 
 TYR   0.027   0.002   TYR A 238 
 PHE   0.016   0.002   PHE A 292 
 TRP   0.016   0.002   TRP A 623 
 HIS   0.006   0.002   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 6963)
  covalent geometry    : angle       0.76293 ( 9537)
  hydrogen bonds       : bond        0.05784 (  254)
  hydrogen bonds       : angle       6.19196 (  711)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.354 
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: A   98 MET cc_start: 0.9251 (mmt) cc_final: 0.9030 (mmt)
REVERT: A  148 LYS cc_start: 0.8108 (mptt) cc_final: 0.7844 (mptt)
REVERT: A  282 ARG cc_start: 0.9309 (tpp80) cc_final: 0.8865 (mmm160)
REVERT: A  304 MET cc_start: 0.8819 (mmm) cc_final: 0.7374 (mmp)
REVERT: A  353 MET cc_start: 0.8497 (ppp) cc_final: 0.8284 (ppp)
REVERT: A  363 MET cc_start: 0.8257 (tpp) cc_final: 0.7752 (tpp)
REVERT: A  466 MET cc_start: 0.9566 (pmm) cc_final: 0.8716 (mpp)
REVERT: A  476 ASN cc_start: 0.9767 (m-40) cc_final: 0.9527 (m-40)
REVERT: A  554 TYR cc_start: 0.7787 (m-80) cc_final: 0.7563 (m-80)
REVERT: A  591 PHE cc_start: 0.9748 (m-80) cc_final: 0.9441 (m-80)
REVERT: A  620 ASP cc_start: 0.9076 (m-30) cc_final: 0.8577 (p0)
REVERT: A  652 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8666 (p0)
REVERT: A  731 LYS cc_start: 0.9698 (mttm) cc_final: 0.9330 (mtmm)
  outliers start: 13
  outliers final: 6
  residues processed: 146
  average time/residue: 0.0958
  time to fit residues: 18.5682
Evaluate side-chains
  120 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  652 ASN
Chi-restraints excluded: chain A residue  681 ASN
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  705 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 63 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 62 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 66 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    3.6986

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 655 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.064442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.050138 restraints weight = 36476.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.052030 restraints weight = 22091.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.053417 restraints weight = 15410.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.054456 restraints weight = 11720.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.055191 restraints weight = 9478.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.4524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.088   6963  Z= 0.274
  Angle     :  0.777   8.171   9537  Z= 0.418
  Chirality :  0.047   0.332   1043
  Planarity :  0.005   0.036   1090
  Dihedral  : 20.319 126.886   1196
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 25.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.66 %
    Favored  : 79.04 %
  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: -1.77 (0.29), residues: 743
  helix: -0.14 (0.34), residues: 221
  sheet: -2.08 (0.43), residues: 124
  loop : -1.43 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 613 
 TYR   0.022   0.002   TYR A 306 
 PHE   0.017   0.003   PHE A 738 
 TRP   0.012   0.002   TRP A 528 
 HIS   0.004   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 ( 6963)
  covalent geometry    : angle       0.77702 ( 9537)
  hydrogen bonds       : bond        0.05311 (  254)
  hydrogen bonds       : angle       6.06474 (  711)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.261 
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   73 LEU cc_start: 0.8907 (mt) cc_final: 0.8531 (mp)
REVERT: A   98 MET cc_start: 0.8968 (mmt) cc_final: 0.8748 (mmt)
REVERT: A  138 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8317 (mm)
REVERT: A  145 ASP cc_start: 0.9256 (p0) cc_final: 0.8844 (p0)
REVERT: A  148 LYS cc_start: 0.8397 (mptt) cc_final: 0.7949 (mptt)
REVERT: A  304 MET cc_start: 0.9086 (mmm) cc_final: 0.8512 (mmp)
REVERT: A  353 MET cc_start: 0.8591 (ppp) cc_final: 0.8376 (ppp)
REVERT: A  363 MET cc_start: 0.8234 (tpp) cc_final: 0.7797 (tpp)
REVERT: A  486 ASN cc_start: 0.9163 (t0) cc_final: 0.8956 (t0)
REVERT: A  554 TYR cc_start: 0.8204 (m-80) cc_final: 0.7797 (m-80)
REVERT: A  591 PHE cc_start: 0.9736 (m-80) cc_final: 0.9392 (m-80)
REVERT: A  711 GLN cc_start: 0.9418 (mm-40) cc_final: 0.9165 (mm110)
REVERT: A  731 LYS cc_start: 0.9639 (mttm) cc_final: 0.9209 (mtpt)
  outliers start: 22
  outliers final: 11
  residues processed: 127
  average time/residue: 0.0979
  time to fit residues: 16.4175
Evaluate side-chains
  108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  365 ILE
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  624 TYR
Chi-restraints excluded: chain A residue  681 ASN
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  705 GLN
Chi-restraints excluded: chain A residue  725 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 47 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 24 optimal weight:    0.2980
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 ASN
A 569 ASN
A 602 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.066963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.051918 restraints weight = 34517.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.053996 restraints weight = 20988.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.055512 restraints weight = 14559.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.056587 restraints weight = 10980.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.057399 restraints weight = 8806.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.4922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   6963  Z= 0.158
  Angle     :  0.707  10.277   9537  Z= 0.367
  Chirality :  0.045   0.174   1043
  Planarity :  0.004   0.033   1090
  Dihedral  : 19.904 122.739   1196
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 18.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 21.11 %
    Favored  : 76.50 %
  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: -1.32 (0.30), residues: 743
  helix:  0.27 (0.35), residues: 225
  sheet: -1.76 (0.43), residues: 125
  loop : -1.22 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 282 
 TYR   0.027   0.002   TYR A 306 
 PHE   0.022   0.002   PHE A 380 
 TRP   0.032   0.004   TRP A 528 
 HIS   0.004   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6963)
  covalent geometry    : angle       0.70739 ( 9537)
  hydrogen bonds       : bond        0.04138 (  254)
  hydrogen bonds       : angle       5.52243 (  711)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.277 
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   98 MET cc_start: 0.9136 (mmt) cc_final: 0.8882 (mmt)
REVERT: A  138 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8378 (mm)
REVERT: A  169 MET cc_start: 0.9215 (ppp) cc_final: 0.8984 (ppp)
REVERT: A  304 MET cc_start: 0.9094 (mmm) cc_final: 0.8546 (mmp)
REVERT: A  353 MET cc_start: 0.8618 (ppp) cc_final: 0.8394 (ppp)
REVERT: A  554 TYR cc_start: 0.8079 (m-80) cc_final: 0.7675 (m-80)
REVERT: A  591 PHE cc_start: 0.9724 (m-80) cc_final: 0.9381 (m-80)
REVERT: A  622 ASP cc_start: 0.9483 (t0) cc_final: 0.9187 (p0)
REVERT: A  731 LYS cc_start: 0.9593 (mttm) cc_final: 0.9118 (mtpt)
  outliers start: 16
  outliers final: 6
  residues processed: 113
  average time/residue: 0.0904
  time to fit residues: 13.8130
Evaluate side-chains
  104 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  681 ASN
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  705 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 41 optimal weight:    5.9990
   chunk 75 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 506 ASN
A 602 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.065671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.050962 restraints weight = 36031.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.052949 restraints weight = 21924.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.054364 restraints weight = 15308.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.055420 restraints weight = 11639.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.056211 restraints weight = 9390.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.5250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   6963  Z= 0.180
  Angle     :  0.679   9.573   9537  Z= 0.355
  Chirality :  0.044   0.160   1043
  Planarity :  0.004   0.050   1090
  Dihedral  : 19.906 123.226   1196
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 20.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 22.01 %
    Favored  : 76.05 %
  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: -1.12 (0.30), residues: 743
  helix:  0.30 (0.34), residues: 227
  sheet: -1.61 (0.44), residues: 124
  loop : -1.02 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 158 
 TYR   0.019   0.002   TYR A 672 
 PHE   0.015   0.002   PHE A 380 
 TRP   0.026   0.003   TRP A 528 
 HIS   0.004   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 6963)
  covalent geometry    : angle       0.67885 ( 9537)
  hydrogen bonds       : bond        0.03935 (  254)
  hydrogen bonds       : angle       5.40094 (  711)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9004 (mmt) cc_final: 0.8779 (mmt)
REVERT: A  138 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8127 (mm)
REVERT: A  148 LYS cc_start: 0.8471 (mmtm) cc_final: 0.8048 (mptt)
REVERT: A  169 MET cc_start: 0.9292 (ppp) cc_final: 0.9048 (ppp)
REVERT: A  304 MET cc_start: 0.9111 (mmm) cc_final: 0.8501 (mmm)
REVERT: A  352 LEU cc_start: 0.9329 (tp) cc_final: 0.9016 (tp)
REVERT: A  353 MET cc_start: 0.8675 (ppp) cc_final: 0.8474 (ppp)
REVERT: A  418 GLU cc_start: 0.9550 (mt-10) cc_final: 0.9275 (mm-30)
REVERT: A  486 ASN cc_start: 0.9098 (t0) cc_final: 0.8891 (t0)
REVERT: A  554 TYR cc_start: 0.8214 (m-80) cc_final: 0.7765 (m-80)
REVERT: A  591 PHE cc_start: 0.9715 (m-80) cc_final: 0.9369 (m-80)
REVERT: A  622 ASP cc_start: 0.9497 (t0) cc_final: 0.9178 (p0)
REVERT: A  694 TYR cc_start: 0.8585 (t80) cc_final: 0.8329 (t80)
REVERT: A  711 GLN cc_start: 0.9413 (mm-40) cc_final: 0.9164 (mm110)
REVERT: A  731 LYS cc_start: 0.9559 (mttm) cc_final: 0.9103 (mtpt)
REVERT: A  734 LYS cc_start: 0.9303 (tppt) cc_final: 0.9094 (tppt)
  outliers start: 13
  outliers final: 8
  residues processed: 112
  average time/residue: 0.0903
  time to fit residues: 13.6541
Evaluate side-chains
  103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  681 ASN
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  705 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 75 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.064199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.049685 restraints weight = 36409.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.051602 restraints weight = 22273.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.053051 restraints weight = 15596.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.054068 restraints weight = 11868.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.054824 restraints weight = 9621.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.5507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.092   6963  Z= 0.207
  Angle     :  0.698  11.692   9537  Z= 0.367
  Chirality :  0.044   0.153   1043
  Planarity :  0.004   0.042   1090
  Dihedral  : 19.918 121.917   1196
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 21.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 22.01 %
    Favored  : 75.60 %
  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: -1.15 (0.30), residues: 743
  helix:  0.27 (0.34), residues: 227
  sheet: -1.60 (0.40), residues: 158
  loop : -0.94 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 161 
 TYR   0.035   0.002   TYR A 306 
 PHE   0.013   0.002   PHE A 458 
 TRP   0.022   0.003   TRP A 528 
 HIS   0.004   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 6963)
  covalent geometry    : angle       0.69756 ( 9537)
  hydrogen bonds       : bond        0.03939 (  254)
  hydrogen bonds       : angle       5.47204 (  711)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.273 
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   98 MET cc_start: 0.8988 (mmt) cc_final: 0.8771 (mmt)
REVERT: A  138 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8171 (mm)
REVERT: A  148 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8129 (mptt)
REVERT: A  169 MET cc_start: 0.9321 (ppp) cc_final: 0.9071 (ppp)
REVERT: A  304 MET cc_start: 0.9081 (mmm) cc_final: 0.8539 (mmm)
REVERT: A  352 LEU cc_start: 0.9328 (tp) cc_final: 0.9013 (tp)
REVERT: A  466 MET cc_start: 0.9672 (pmm) cc_final: 0.8779 (mpp)
REVERT: A  486 ASN cc_start: 0.9124 (t0) cc_final: 0.8895 (t0)
REVERT: A  554 TYR cc_start: 0.8265 (m-80) cc_final: 0.7796 (m-80)
REVERT: A  591 PHE cc_start: 0.9699 (m-80) cc_final: 0.9349 (m-80)
REVERT: A  622 ASP cc_start: 0.9492 (t0) cc_final: 0.9209 (p0)
REVERT: A  694 TYR cc_start: 0.8599 (t80) cc_final: 0.8300 (t80)
REVERT: A  711 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9151 (mm110)
REVERT: A  731 LYS cc_start: 0.9579 (mttm) cc_final: 0.9146 (mtpt)
  outliers start: 16
  outliers final: 9
  residues processed: 110
  average time/residue: 0.0788
  time to fit residues: 12.0845
Evaluate side-chains
  104 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  681 ASN
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  705 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.064474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.049879 restraints weight = 34826.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.051793 restraints weight = 21563.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.053213 restraints weight = 15179.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.054258 restraints weight = 11599.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.055022 restraints weight = 9377.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.5744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   6963  Z= 0.179
  Angle     :  0.674  10.102   9537  Z= 0.356
  Chirality :  0.043   0.150   1043
  Planarity :  0.004   0.031   1090
  Dihedral  : 19.848 121.250   1196
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 21.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 24.10 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.30), residues: 743
  helix:  0.32 (0.34), residues: 227
  sheet: -1.26 (0.46), residues: 124
  loop : -0.84 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 161 
 TYR   0.025   0.002   TYR A 306 
 PHE   0.014   0.002   PHE A 458 
 TRP   0.018   0.003   TRP A 482 
 HIS   0.004   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6963)
  covalent geometry    : angle       0.67427 ( 9537)
  hydrogen bonds       : bond        0.03740 (  254)
  hydrogen bonds       : angle       5.45314 (  711)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.263 
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   98 MET cc_start: 0.8979 (mmt) cc_final: 0.8770 (mmt)
REVERT: A  138 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8146 (mm)
REVERT: A  148 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8077 (mptt)
REVERT: A  159 LYS cc_start: 0.9544 (ttpp) cc_final: 0.9341 (ttpp)
REVERT: A  169 MET cc_start: 0.9318 (ppp) cc_final: 0.9074 (ppp)
REVERT: A  270 MET cc_start: 0.3840 (pmm) cc_final: 0.3479 (pmm)
REVERT: A  304 MET cc_start: 0.9018 (mmm) cc_final: 0.8533 (mmm)
REVERT: A  317 ASP cc_start: 0.9287 (m-30) cc_final: 0.8996 (t0)
REVERT: A  363 MET cc_start: 0.8859 (tpt) cc_final: 0.8532 (tpt)
REVERT: A  466 MET cc_start: 0.9662 (pmm) cc_final: 0.8774 (mpp)
REVERT: A  486 ASN cc_start: 0.9127 (t0) cc_final: 0.8885 (t0)
REVERT: A  544 ASP cc_start: 0.8615 (t0) cc_final: 0.8235 (m-30)
REVERT: A  554 TYR cc_start: 0.8341 (m-80) cc_final: 0.7909 (m-80)
REVERT: A  591 PHE cc_start: 0.9685 (m-10) cc_final: 0.9316 (m-80)
REVERT: A  622 ASP cc_start: 0.9487 (t0) cc_final: 0.9221 (p0)
REVERT: A  694 TYR cc_start: 0.8656 (t80) cc_final: 0.8369 (t80)
REVERT: A  731 LYS cc_start: 0.9591 (mttm) cc_final: 0.9158 (mtpt)
  outliers start: 15
  outliers final: 8
  residues processed: 107
  average time/residue: 0.0864
  time to fit residues: 12.8960
Evaluate side-chains
  103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  681 ASN
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  705 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:    0.3980
   chunk 61 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 54 optimal weight:   20.0000
   chunk 4 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   overall best weight:    3.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.062181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.047887 restraints weight = 37378.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.049763 restraints weight = 22968.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.051154 restraints weight = 16123.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.052171 restraints weight = 12302.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.052916 restraints weight = 9964.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.5988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   6963  Z= 0.234
  Angle     :  0.695   9.142   9537  Z= 0.372
  Chirality :  0.044   0.151   1043
  Planarity :  0.004   0.044   1090
  Dihedral  : 19.931 121.048   1196
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 24.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 23.65 %
    Favored  : 74.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.94 (0.30), residues: 743
  helix:  0.12 (0.34), residues: 228
  sheet: -1.11 (0.47), residues: 126
  loop : -0.83 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 161 
 TYR   0.028   0.002   TYR A 306 
 PHE   0.015   0.002   PHE A 616 
 TRP   0.026   0.003   TRP A 528 
 HIS   0.006   0.002   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 6963)
  covalent geometry    : angle       0.69523 ( 9537)
  hydrogen bonds       : bond        0.04133 (  254)
  hydrogen bonds       : angle       5.60097 (  711)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8295 (mm)
REVERT: A  148 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8203 (mptt)
REVERT: A  159 LYS cc_start: 0.9556 (ttpp) cc_final: 0.9298 (ttpp)
REVERT: A  169 MET cc_start: 0.9335 (ppp) cc_final: 0.9057 (ppp)
REVERT: A  270 MET cc_start: 0.4286 (pmm) cc_final: 0.3926 (pmm)
REVERT: A  304 MET cc_start: 0.8861 (mmm) cc_final: 0.8406 (mmm)
REVERT: A  363 MET cc_start: 0.8877 (tpt) cc_final: 0.8561 (tpt)
REVERT: A  453 TYR cc_start: 0.9456 (m-80) cc_final: 0.9206 (m-80)
REVERT: A  466 MET cc_start: 0.9645 (pmm) cc_final: 0.9434 (pmm)
REVERT: A  554 TYR cc_start: 0.8376 (m-80) cc_final: 0.7949 (m-80)
REVERT: A  591 PHE cc_start: 0.9652 (m-10) cc_final: 0.9340 (m-80)
REVERT: A  622 ASP cc_start: 0.9474 (t0) cc_final: 0.9215 (p0)
REVERT: A  694 TYR cc_start: 0.8654 (t80) cc_final: 0.8370 (t80)
REVERT: A  731 LYS cc_start: 0.9643 (mttm) cc_final: 0.9217 (mtpt)
  outliers start: 14
  outliers final: 8
  residues processed: 104
  average time/residue: 0.0833
  time to fit residues: 12.0256
Evaluate side-chains
  100 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  681 ASN
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  705 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 35 optimal weight:    0.0970
   chunk 27 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 1 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 7 optimal weight:    9.9990
   overall best weight:    1.4182

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.064081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.049505 restraints weight = 35541.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.051469 restraints weight = 21767.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.052907 restraints weight = 15261.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.053994 restraints weight = 11602.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.054772 restraints weight = 9325.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.6177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6963  Z= 0.153
  Angle     :  0.683   9.180   9537  Z= 0.360
  Chirality :  0.044   0.155   1043
  Planarity :  0.004   0.037   1090
  Dihedral  : 19.794 121.823   1196
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 25.00 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.30), residues: 743
  helix:  0.15 (0.34), residues: 227
  sheet: -0.73 (0.48), residues: 125
  loop : -0.78 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 747 
 TYR   0.031   0.002   TYR A 306 
 PHE   0.013   0.002   PHE A 458 
 TRP   0.021   0.003   TRP A 528 
 HIS   0.004   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6963)
  covalent geometry    : angle       0.68327 ( 9537)
  hydrogen bonds       : bond        0.03729 (  254)
  hydrogen bonds       : angle       5.51728 (  711)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.7992 (mm)
REVERT: A  148 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8159 (mptt)
REVERT: A  169 MET cc_start: 0.9199 (ppp) cc_final: 0.8872 (ppp)
REVERT: A  270 MET cc_start: 0.4373 (pmm) cc_final: 0.4073 (pmm)
REVERT: A  302 MET cc_start: 0.8740 (tpt) cc_final: 0.8431 (tpt)
REVERT: A  304 MET cc_start: 0.8801 (mmm) cc_final: 0.8439 (mmm)
REVERT: A  317 ASP cc_start: 0.9225 (m-30) cc_final: 0.8988 (t0)
REVERT: A  363 MET cc_start: 0.8680 (tpt) cc_final: 0.8353 (tpt)
REVERT: A  466 MET cc_start: 0.9619 (pmm) cc_final: 0.8757 (mpp)
REVERT: A  533 MET cc_start: 0.8205 (tpp) cc_final: 0.7949 (tmm)
REVERT: A  554 TYR cc_start: 0.8330 (m-80) cc_final: 0.7900 (m-80)
REVERT: A  591 PHE cc_start: 0.9642 (m-10) cc_final: 0.9292 (m-80)
REVERT: A  622 ASP cc_start: 0.9439 (t0) cc_final: 0.9187 (p0)
REVERT: A  694 TYR cc_start: 0.8636 (t80) cc_final: 0.8379 (t80)
REVERT: A  711 GLN cc_start: 0.9413 (mm-40) cc_final: 0.9082 (mm110)
REVERT: A  731 LYS cc_start: 0.9650 (mttm) cc_final: 0.9213 (mtpt)
  outliers start: 10
  outliers final: 8
  residues processed: 108
  average time/residue: 0.0843
  time to fit residues: 12.5173
Evaluate side-chains
  105 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  681 ASN
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  705 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 31 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 13 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 68 optimal weight:    8.9990
   chunk 7 optimal weight:    8.9990
   chunk 44 optimal weight:    0.0000
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.9590

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.065508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.050727 restraints weight = 34796.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.052684 restraints weight = 21673.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.054122 restraints weight = 15354.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.055173 restraints weight = 11747.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.055988 restraints weight = 9518.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.6358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6963  Z= 0.139
  Angle     :  0.691   9.745   9537  Z= 0.360
  Chirality :  0.044   0.166   1043
  Planarity :  0.004   0.060   1090
  Dihedral  : 19.701 122.291   1196
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 17.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 24.85 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.78 (0.30), residues: 743
  helix:  0.14 (0.34), residues: 223
  sheet: -0.71 (0.47), residues: 126
  loop : -0.76 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 161 
 TYR   0.026   0.002   TYR A 306 
 PHE   0.012   0.001   PHE A 458 
 TRP   0.019   0.003   TRP A 528 
 HIS   0.003   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6963)
  covalent geometry    : angle       0.69074 ( 9537)
  hydrogen bonds       : bond        0.03751 (  254)
  hydrogen bonds       : angle       5.45165 (  711)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.7929 (mm)
REVERT: A  148 LYS cc_start: 0.8740 (mmtm) cc_final: 0.8065 (mptt)
REVERT: A  169 MET cc_start: 0.9051 (ppp) cc_final: 0.8806 (ppp)
REVERT: A  270 MET cc_start: 0.4330 (pmm) cc_final: 0.3992 (pmm)
REVERT: A  302 MET cc_start: 0.8755 (tpt) cc_final: 0.8443 (tpt)
REVERT: A  304 MET cc_start: 0.8810 (mmm) cc_final: 0.8421 (mmm)
REVERT: A  317 ASP cc_start: 0.9304 (m-30) cc_final: 0.9047 (t0)
REVERT: A  363 MET cc_start: 0.8579 (tpt) cc_final: 0.8292 (tpt)
REVERT: A  466 MET cc_start: 0.9650 (pmm) cc_final: 0.8782 (mpp)
REVERT: A  533 MET cc_start: 0.8199 (tpp) cc_final: 0.7785 (tmm)
REVERT: A  554 TYR cc_start: 0.8362 (m-80) cc_final: 0.7923 (m-80)
REVERT: A  591 PHE cc_start: 0.9610 (m-10) cc_final: 0.9253 (m-80)
REVERT: A  622 ASP cc_start: 0.9470 (t0) cc_final: 0.9220 (p0)
REVERT: A  694 TYR cc_start: 0.8665 (t80) cc_final: 0.8382 (t80)
REVERT: A  711 GLN cc_start: 0.9327 (mm-40) cc_final: 0.8983 (mm110)
REVERT: A  728 TYR cc_start: 0.9706 (m-10) cc_final: 0.9330 (m-80)
REVERT: A  731 LYS cc_start: 0.9630 (mttm) cc_final: 0.9200 (mtpt)
  outliers start: 11
  outliers final: 8
  residues processed: 108
  average time/residue: 0.0786
  time to fit residues: 11.8381
Evaluate side-chains
  107 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  681 ASN
Chi-restraints excluded: chain A residue  703 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 54 optimal weight:   30.0000
   chunk 26 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.065969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.051334 restraints weight = 35740.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.053241 restraints weight = 22027.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.054672 restraints weight = 15491.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.055758 restraints weight = 11865.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.056538 restraints weight = 9575.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.6506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6963  Z= 0.148
  Angle     :  0.687  10.209   9537  Z= 0.357
  Chirality :  0.044   0.147   1043
  Planarity :  0.004   0.057   1090
  Dihedral  : 19.657 122.222   1196
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 18.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 25.15 %
    Favored  : 72.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.30), residues: 743
  helix:  0.26 (0.34), residues: 225
  sheet: -0.47 (0.47), residues: 128
  loop : -0.72 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 161 
 TYR   0.026   0.002   TYR A 306 
 PHE   0.013   0.001   PHE A 458 
 TRP   0.019   0.002   TRP A 528 
 HIS   0.004   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6963)
  covalent geometry    : angle       0.68661 ( 9537)
  hydrogen bonds       : bond        0.03633 (  254)
  hydrogen bonds       : angle       5.36946 (  711)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1325.30 seconds
wall clock time: 23 minutes 51.57 seconds (1431.57 seconds total)