Starting phenix.real_space_refine
on Tue Jul 29 00:00:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8emv_28266/07_2025/8emv_28266.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8emv_28266/07_2025/8emv_28266.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8emv_28266/07_2025/8emv_28266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8emv_28266/07_2025/8emv_28266.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8emv_28266/07_2025/8emv_28266.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8emv_28266/07_2025/8emv_28266.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5939 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      31      5.16       5
     C    3795      2.51       5
     N    1013      2.21       5
     O    1109      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5949
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 747, 5948
          Classifications: {'peptide': 747}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 47, 'TRANS': 699}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.85, per 1000 atoms: 0.82
  Number of scatterers: 5949
  At special positions: 0
  Unit cell: (62.64, 98.28, 103.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      31     16.00
     O    1109      8.00
     N    1013      7.00
     C    3795      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: 2.03
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1418

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 6 sheets defined
      33.3% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 25
      removed outlier: 3.743A  pdb=" N   ARG A  24 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 127 through 140
    Processing helix  chain 'A' and resid 148 through 163
      removed outlier: 3.503A  pdb=" N   PHE A 152 " --> pdb=" O   SER A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 179
      removed outlier: 4.287A  pdb=" N   ILE A 175 " --> pdb=" O   PRO A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 194
      removed outlier: 3.641A  pdb=" N   GLU A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 208
    Processing helix  chain 'A' and resid 209 through 221
    Processing helix  chain 'A' and resid 223 through 233
      removed outlier: 3.662A  pdb=" N   ASP A 227 " --> pdb=" O   ARG A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 253
    Processing helix  chain 'A' and resid 268 through 280
      removed outlier: 4.887A  pdb=" N   LEU A 274 " --> pdb=" O   SER A 270 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   LEU A 275 " --> pdb=" O   GLN A 271 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ILE A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 288
      removed outlier: 3.736A  pdb=" N   GLU A 287 " --> pdb=" O   GLN A 283 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ARG A 288 " --> pdb=" O   GLN A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 300
      removed outlier: 3.639A  pdb=" N   ARG A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 324
      No H-bonds generated for 'chain 'A' and resid 322 through 324'
    Processing helix  chain 'A' and resid 347 through 357
      removed outlier: 3.927A  pdb=" N   ARG A 351 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 399
    Processing helix  chain 'A' and resid 418 through 434
      removed outlier: 3.672A  pdb=" N   PHE A 433 " --> pdb=" O   CYS A 429 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY A 434 " --> pdb=" O   ARG A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 611
    Processing helix  chain 'A' and resid 622 through 632
    Processing helix  chain 'A' and resid 632 through 641
    Processing helix  chain 'A' and resid 661 through 666
    Processing helix  chain 'A' and resid 680 through 690
    Processing helix  chain 'A' and resid 702 through 706
      removed outlier: 3.674A  pdb=" N   ARG A 706 " --> pdb=" O   GLU A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 816
      No H-bonds generated for 'chain 'A' and resid 814 through 816'
    Processing helix  chain 'A' and resid 868 through 881
      removed outlier: 4.689A  pdb=" N   ALA A 878 " --> pdb=" O   ARG A 874 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   LEU A 879 " --> pdb=" O   GLN A 875 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65
      removed outlier: 4.116A  pdb=" N   THR A  55 " --> pdb=" O   THR A  42 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   THR A  42 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER A  26 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 328
    Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 388
      removed outlier: 6.706A  pdb=" N   VAL A 361 " --> pdb=" O   SER A 411 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   GLU A 413 " --> pdb=" O   VAL A 361 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU A 363 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 598 through 599
      removed outlier: 5.978A  pdb=" N   GLU A 598 " --> pdb=" O   MET A 617 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   SER A 619 " --> pdb=" O   GLU A 598 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU A 644 " --> pdb=" O   GLU A 616 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER A 618 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A 671 " --> pdb=" O   SER A 645 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 781 through 786
      removed outlier: 4.518A  pdb=" N   LYS A 785 " --> pdb=" O   ASN A 726 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ASN A 726 " --> pdb=" O   LYS A 785 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LEU A 839 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   GLY A 735 " --> pdb=" O   ALA A 837 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ALA A 837 " --> pdb=" O   GLY A 735 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 759 through 763
      removed outlier: 5.058A  pdb=" N   LYS A 761 " --> pdb=" O   VAL A 749 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   VAL A 749 " --> pdb=" O   LYS A 761 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   ARG A 763 " --> pdb=" O   VAL A 747 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   VAL A 747 " --> pdb=" O   ARG A 763 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   GLU A 800 " --> pdb=" O   PHE A 805 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   PHE A 805 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)

    201 hydrogen bonds defined for protein.
    570 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.63

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1898
        1.34 -     1.45: 878
        1.45 -     1.57: 3246
        1.57 -     1.69: 0
        1.69 -     1.81: 53
  Bond restraints: 6075
  Sorted by residual:
  bond pdb=" C   PRO A 370 "
       pdb=" N   PRO A 371 "
    ideal  model  delta    sigma   weight residual
    1.336  1.390 -0.054 1.20e-02 6.94e+03 2.04e+01
  bond pdb=" C   PRO A 454 "
       pdb=" N   SER A 455 "
    ideal  model  delta    sigma   weight residual
    1.329  1.233  0.095 3.03e-02 1.09e+03 9.92e+00
  bond pdb=" C   LEU A 835 "
       pdb=" N   PRO A 836 "
    ideal  model  delta    sigma   weight residual
    1.333  1.349 -0.016 1.17e-02 7.31e+03 1.99e+00
  bond pdb=" CB  CYS A 669 "
       pdb=" SG  CYS A 669 "
    ideal  model  delta    sigma   weight residual
    1.808  1.763  0.045 3.30e-02 9.18e+02 1.85e+00
  bond pdb=" C   LEU A 453 "
       pdb=" N   PRO A 454 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.016 1.25e-02 6.40e+03 1.72e+00
  ... (remaining 6070 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 7808
        1.66 -     3.31: 353
        3.31 -     4.97: 54
        4.97 -     6.63: 6
        6.63 -     8.28: 6
  Bond angle restraints: 8227
  Sorted by residual:
  angle pdb=" C   SER A 200 "
        pdb=" N   GLU A 201 "
        pdb=" CA  GLU A 201 "
      ideal   model   delta    sigma   weight residual
     121.54  129.14   -7.60 1.91e+00 2.74e-01 1.59e+01
  angle pdb=" C   GLY A 380 "
        pdb=" N   PHE A 381 "
        pdb=" CA  PHE A 381 "
      ideal   model   delta    sigma   weight residual
     122.82  128.33   -5.51 1.42e+00 4.96e-01 1.50e+01
  angle pdb=" N   LEU A 835 "
        pdb=" CA  LEU A 835 "
        pdb=" C   LEU A 835 "
      ideal   model   delta    sigma   weight residual
     109.81  117.69   -7.88 2.21e+00 2.05e-01 1.27e+01
  angle pdb=" N   PRO A 370 "
        pdb=" CA  PRO A 370 "
        pdb=" C   PRO A 370 "
      ideal   model   delta    sigma   weight residual
     110.70  114.57   -3.87 1.22e+00 6.72e-01 1.00e+01
  angle pdb=" CA  PRO A 370 "
        pdb=" C   PRO A 370 "
        pdb=" N   PRO A 371 "
      ideal   model   delta    sigma   weight residual
     117.93  121.50   -3.57 1.20e+00 6.94e-01 8.86e+00
  ... (remaining 8222 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.47: 3225
       16.47 -    32.94: 405
       32.94 -    49.41: 65
       49.41 -    65.88: 23
       65.88 -    82.35: 7
  Dihedral angle restraints: 3725
    sinusoidal: 1539
      harmonic: 2186
  Sorted by residual:
  dihedral pdb=" CA  LYS A 238 "
           pdb=" C   LYS A 238 "
           pdb=" N   PRO A 239 "
           pdb=" CA  PRO A 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.53  -29.47     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  LYS A 236 "
           pdb=" C   LYS A 236 "
           pdb=" N   GLY A 237 "
           pdb=" CA  GLY A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.95   24.05     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  PRO A 239 "
           pdb=" C   PRO A 239 "
           pdb=" N   TYR A 240 "
           pdb=" CA  TYR A 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.69  -19.31     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 3722 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 548
       0.039 -    0.078: 254
       0.078 -    0.117: 77
       0.117 -    0.156: 26
       0.156 -    0.195: 10
  Chirality restraints: 915
  Sorted by residual:
  chirality pdb=" CB  VAL A 116 "
            pdb=" CA  VAL A 116 "
            pdb=" CG1 VAL A 116 "
            pdb=" CG2 VAL A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.19 2.00e-01 2.50e+01 9.46e-01
  chirality pdb=" CB  VAL A 621 "
            pdb=" CA  VAL A 621 "
            pdb=" CG1 VAL A 621 "
            pdb=" CG2 VAL A 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.22e-01
  chirality pdb=" CA  LEU A 835 "
            pdb=" N   LEU A 835 "
            pdb=" C   LEU A 835 "
            pdb=" CB  LEU A 835 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.71e-01
  ... (remaining 912 not shown)

  Planarity restraints: 1071
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 369 "    0.046 5.00e-02 4.00e+02   6.97e-02 7.77e+00
        pdb=" N   PRO A 370 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 370 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 370 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 111 "   -0.041 5.00e-02 4.00e+02   6.07e-02 5.89e+00
        pdb=" N   PRO A 112 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 112 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 112 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 321 "   -0.037 5.00e-02 4.00e+02   5.56e-02 4.95e+00
        pdb=" N   PRO A 322 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1068 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2031
        2.85 -     3.36: 5011
        3.36 -     3.88: 9084
        3.88 -     4.39: 10476
        4.39 -     4.90: 18462
  Nonbonded interactions: 45064
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 225 "
            pdb=" OD1 ASP A 225 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" O   SER A 591 "
            pdb=" OG  SER A 591 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" OE1 GLU A 577 "
            pdb=" OG  SER A 581 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" N   ASP A 125 "
            pdb=" OD1 ASP A 125 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" O   SER A 404 "
            pdb=" OG  SER A 404 "
     model   vdw
     2.382 3.040
  ... (remaining 45059 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             155.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     34.180
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:5.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  195.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
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      :  0.007   0.095   6075  Z= 0.300
  Angle     :  0.813   8.282   8227  Z= 0.461
  Chirality :  0.052   0.195    915
  Planarity :  0.007   0.070   1071
  Dihedral  : 15.162  82.355   2307
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.26 (0.24), residues: 739
  helix: -3.01 (0.23), residues: 235
  sheet: -2.29 (0.41), residues: 124
  loop : -2.89 (0.26), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  54 
 HIS   0.005   0.001   HIS A 808 
 PHE   0.018   0.002   PHE A 799 
 TYR   0.019   0.002   TYR A 648 
 ARG   0.012   0.001   ARG A  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21576 (  201)
  hydrogen bonds       : angle       7.21270 (  570)
  covalent geometry    : bond        0.00705 ( 6075)
  covalent geometry    : angle       0.81279 ( 8227)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A  228 LYS cc_start: 0.8684 (tttt) cc_final: 0.8369 (tptp)
REVERT: A  291 MET cc_start: 0.8471 (ttm) cc_final: 0.8129 (ttm)
REVERT: A  444 LYS cc_start: 0.8438 (tttm) cc_final: 0.8071 (tptm)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.4059
  time to fit residues: 42.4946
Evaluate side-chains
  56 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   chunk 22 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 166 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.106591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.082070 restraints weight = 9063.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.084314 restraints weight = 6007.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.085874 restraints weight = 4639.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6075  Z= 0.114
  Angle     :  0.524   5.390   8227  Z= 0.277
  Chirality :  0.042   0.151    915
  Planarity :  0.005   0.045   1071
  Dihedral  :  4.677  25.877    816
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.40 %
    Favored  : 88.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.27), residues: 739
  helix: -0.95 (0.31), residues: 237
  sheet: -1.78 (0.41), residues: 130
  loop : -2.29 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 131 
 HIS   0.002   0.000   HIS A 808 
 PHE   0.030   0.001   PHE A 197 
 TYR   0.012   0.001   TYR A 820 
 ARG   0.003   0.000   ARG A  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04251 (  201)
  hydrogen bonds       : angle       4.92870 (  570)
  covalent geometry    : bond        0.00261 ( 6075)
  covalent geometry    : angle       0.52414 ( 8227)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A  291 MET cc_start: 0.8539 (ttm) cc_final: 0.8272 (ttm)
REVERT: A  444 LYS cc_start: 0.8462 (tttm) cc_final: 0.8068 (tptm)
REVERT: A  719 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8767 (mm)
REVERT: A  772 PHE cc_start: 0.7928 (t80) cc_final: 0.7703 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 77
  average time/residue: 0.2099
  time to fit residues: 20.9880
Evaluate side-chains
  66 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  652 THR
Chi-restraints excluded: chain A residue  719 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 36 optimal weight:    0.3980
   chunk 16 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 55 optimal weight:    0.1980
   chunk 69 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.108709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.084277 restraints weight = 9114.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.086580 restraints weight = 6048.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.088154 restraints weight = 4669.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6075  Z= 0.099
  Angle     :  0.501   6.621   8227  Z= 0.256
  Chirality :  0.042   0.169    915
  Planarity :  0.004   0.049   1071
  Dihedral  :  4.234  24.189    816
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 11.01 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.29), residues: 739
  helix:  0.13 (0.34), residues: 238
  sheet: -1.11 (0.45), residues: 130
  loop : -2.01 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 131 
 HIS   0.002   0.000   HIS A 808 
 PHE   0.028   0.001   PHE A 197 
 TYR   0.010   0.001   TYR A 299 
 ARG   0.003   0.000   ARG A  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03553 (  201)
  hydrogen bonds       : angle       4.44295 (  570)
  covalent geometry    : bond        0.00229 ( 6075)
  covalent geometry    : angle       0.50067 ( 8227)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8472 (ttm) cc_final: 0.8250 (ttm)
REVERT: A  444 LYS cc_start: 0.8455 (tttm) cc_final: 0.7967 (tptm)
REVERT: A  655 ASP cc_start: 0.8045 (p0) cc_final: 0.7575 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 76
  average time/residue: 0.2011
  time to fit residues: 20.6780
Evaluate side-chains
  70 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 42 optimal weight:    0.1980
   chunk 0 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.110950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.086773 restraints weight = 9192.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.089062 restraints weight = 6050.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.090495 restraints weight = 4666.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6075  Z= 0.098
  Angle     :  0.484   5.944   8227  Z= 0.247
  Chirality :  0.041   0.162    915
  Planarity :  0.004   0.048   1071
  Dihedral  :  4.003  23.437    816
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 11.93 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.30), residues: 739
  helix:  0.63 (0.35), residues: 238
  sheet: -0.92 (0.45), residues: 131
  loop : -1.69 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 131 
 HIS   0.002   0.000   HIS A 808 
 PHE   0.029   0.001   PHE A 197 
 TYR   0.009   0.001   TYR A 299 
 ARG   0.003   0.000   ARG A  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03207 (  201)
  hydrogen bonds       : angle       4.18665 (  570)
  covalent geometry    : bond        0.00226 ( 6075)
  covalent geometry    : angle       0.48382 ( 8227)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.8463 (tttm) cc_final: 0.8034 (tptm)
REVERT: A  655 ASP cc_start: 0.8038 (p0) cc_final: 0.7666 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 80
  average time/residue: 0.2134
  time to fit residues: 22.4816
Evaluate side-chains
  73 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 18 optimal weight:    9.9990
   chunk 52 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0070
   chunk 9 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 71 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.110108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.083481 restraints weight = 9254.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.086419 restraints weight = 5398.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.088348 restraints weight = 3872.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6075  Z= 0.091
  Angle     :  0.481   6.414   8227  Z= 0.244
  Chirality :  0.041   0.164    915
  Planarity :  0.004   0.048   1071
  Dihedral  :  3.902  22.943    816
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.30 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.31), residues: 739
  helix:  0.88 (0.36), residues: 238
  sheet: -0.90 (0.44), residues: 129
  loop : -1.43 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 131 
 HIS   0.001   0.000   HIS A 808 
 PHE   0.029   0.001   PHE A 197 
 TYR   0.008   0.001   TYR A 746 
 ARG   0.002   0.000   ARG A  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03011 (  201)
  hydrogen bonds       : angle       4.06690 (  570)
  covalent geometry    : bond        0.00212 ( 6075)
  covalent geometry    : angle       0.48052 ( 8227)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8499 (ttm) cc_final: 0.8037 (tpp)
REVERT: A  444 LYS cc_start: 0.8461 (tttm) cc_final: 0.8042 (tptm)
REVERT: A  655 ASP cc_start: 0.8065 (p0) cc_final: 0.7699 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 80
  average time/residue: 0.2179
  time to fit residues: 23.0097
Evaluate side-chains
  74 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0970
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 254 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.105098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.079524 restraints weight = 9175.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.081811 restraints weight = 6075.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.083214 restraints weight = 4700.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6075  Z= 0.134
  Angle     :  0.506   6.608   8227  Z= 0.258
  Chirality :  0.042   0.161    915
  Planarity :  0.004   0.049   1071
  Dihedral  :  4.047  23.098    816
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.91 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.31), residues: 739
  helix:  1.01 (0.36), residues: 238
  sheet: -0.98 (0.44), residues: 124
  loop : -1.48 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  54 
 HIS   0.003   0.001   HIS A 808 
 PHE   0.029   0.001   PHE A 197 
 TYR   0.011   0.001   TYR A 299 
 ARG   0.003   0.000   ARG A  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03500 (  201)
  hydrogen bonds       : angle       4.16075 (  570)
  covalent geometry    : bond        0.00326 ( 6075)
  covalent geometry    : angle       0.50597 ( 8227)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8070 (tt0)
REVERT: A  444 LYS cc_start: 0.8473 (tttm) cc_final: 0.8021 (tptm)
REVERT: A  655 ASP cc_start: 0.8079 (p0) cc_final: 0.7710 (t0)
REVERT: A  778 GLU cc_start: 0.7155 (pm20) cc_final: 0.6869 (pm20)
  outliers start: 13
  outliers final: 11
  residues processed: 74
  average time/residue: 0.1863
  time to fit residues: 18.3271
Evaluate side-chains
  74 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0270
   overall best weight:    0.6438

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.110087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.083529 restraints weight = 9202.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.086288 restraints weight = 5379.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.088295 restraints weight = 3897.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6075  Z= 0.093
  Angle     :  0.488   7.101   8227  Z= 0.247
  Chirality :  0.042   0.169    915
  Planarity :  0.004   0.049   1071
  Dihedral  :  3.887  21.873    816
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.37 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.31), residues: 739
  helix:  1.28 (0.36), residues: 232
  sheet: -0.87 (0.44), residues: 124
  loop : -1.28 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 776 
 HIS   0.001   0.000   HIS A 808 
 PHE   0.031   0.001   PHE A 197 
 TYR   0.009   0.001   TYR A 746 
 ARG   0.002   0.000   ARG A 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02976 (  201)
  hydrogen bonds       : angle       4.02909 (  570)
  covalent geometry    : bond        0.00217 ( 6075)
  covalent geometry    : angle       0.48836 ( 8227)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.8464 (tttm) cc_final: 0.8084 (tptm)
REVERT: A  655 ASP cc_start: 0.7954 (p0) cc_final: 0.7637 (t0)
REVERT: A  778 GLU cc_start: 0.7135 (pm20) cc_final: 0.6877 (pm20)
  outliers start: 15
  outliers final: 12
  residues processed: 76
  average time/residue: 0.2114
  time to fit residues: 21.1744
Evaluate side-chains
  72 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  614 CYS
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 73 optimal weight:    0.4980
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0070
   chunk 54 optimal weight:    0.2980
   chunk 47 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.7200

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.111254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.086803 restraints weight = 9115.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.089041 restraints weight = 6043.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.090546 restraints weight = 4686.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6075  Z= 0.101
  Angle     :  0.493   7.454   8227  Z= 0.251
  Chirality :  0.042   0.168    915
  Planarity :  0.004   0.050   1071
  Dihedral  :  3.860  21.769    816
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.53 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.31), residues: 739
  helix:  1.39 (0.36), residues: 232
  sheet: -0.84 (0.43), residues: 124
  loop : -1.19 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 776 
 HIS   0.001   0.000   HIS A 808 
 PHE   0.031   0.001   PHE A 197 
 TYR   0.009   0.001   TYR A 746 
 ARG   0.001   0.000   ARG A 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03063 (  201)
  hydrogen bonds       : angle       4.06743 (  570)
  covalent geometry    : bond        0.00242 ( 6075)
  covalent geometry    : angle       0.49266 ( 8227)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8661 (ttm) cc_final: 0.8133 (tpp)
REVERT: A  444 LYS cc_start: 0.8460 (tttm) cc_final: 0.8099 (tptm)
REVERT: A  655 ASP cc_start: 0.7917 (p0) cc_final: 0.7635 (t0)
REVERT: A  778 GLU cc_start: 0.7065 (pm20) cc_final: 0.6821 (pm20)
  outliers start: 15
  outliers final: 12
  residues processed: 72
  average time/residue: 0.2237
  time to fit residues: 21.0237
Evaluate side-chains
  70 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  614 CYS
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0020
   chunk 36 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0270
   chunk 46 optimal weight:    9.9990
   chunk 24 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0270
   chunk 49 optimal weight:    0.9980
   overall best weight:    1.0106

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.107441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.082669 restraints weight = 9207.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.084874 restraints weight = 6199.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.086332 restraints weight = 4817.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6075  Z= 0.122
  Angle     :  0.518   7.584   8227  Z= 0.262
  Chirality :  0.042   0.164    915
  Planarity :  0.004   0.050   1071
  Dihedral  :  3.931  21.586    816
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.29 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.31), residues: 739
  helix:  1.42 (0.36), residues: 232
  sheet: -0.80 (0.43), residues: 124
  loop : -1.17 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  54 
 HIS   0.002   0.001   HIS A 808 
 PHE   0.033   0.001   PHE A 197 
 TYR   0.010   0.001   TYR A 299 
 ARG   0.004   0.000   ARG A 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03308 (  201)
  hydrogen bonds       : angle       4.14113 (  570)
  covalent geometry    : bond        0.00296 ( 6075)
  covalent geometry    : angle       0.51754 ( 8227)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8647 (ttm) cc_final: 0.8148 (tpp)
REVERT: A  444 LYS cc_start: 0.8471 (tttm) cc_final: 0.8104 (tptm)
REVERT: A  655 ASP cc_start: 0.7973 (p0) cc_final: 0.7664 (t0)
  outliers start: 12
  outliers final: 12
  residues processed: 66
  average time/residue: 0.2726
  time to fit residues: 24.0801
Evaluate side-chains
  69 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  614 CYS
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0980
   chunk 20 optimal weight:    0.0980
   chunk 0 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.107856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.083079 restraints weight = 9218.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.085300 restraints weight = 6154.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.086803 restraints weight = 4795.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6075  Z= 0.106
  Angle     :  0.503   7.937   8227  Z= 0.256
  Chirality :  0.042   0.159    915
  Planarity :  0.004   0.050   1071
  Dihedral  :  3.848  21.056    816
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.14 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.31), residues: 739
  helix:  1.55 (0.36), residues: 232
  sheet: -0.65 (0.43), residues: 129
  loop : -1.11 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A  54 
 HIS   0.002   0.000   HIS A 808 
 PHE   0.032   0.001   PHE A 197 
 TYR   0.009   0.001   TYR A 746 
 ARG   0.003   0.000   ARG A 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03075 (  201)
  hydrogen bonds       : angle       4.08393 (  570)
  covalent geometry    : bond        0.00254 ( 6075)
  covalent geometry    : angle       0.50293 ( 8227)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8638 (ttm) cc_final: 0.8151 (tpp)
REVERT: A  444 LYS cc_start: 0.8497 (tttm) cc_final: 0.8169 (tptm)
REVERT: A  655 ASP cc_start: 0.7918 (p0) cc_final: 0.7644 (t0)
  outliers start: 12
  outliers final: 12
  residues processed: 68
  average time/residue: 0.2428
  time to fit residues: 21.9368
Evaluate side-chains
  70 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  614 CYS
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0970
   chunk 34 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 55 optimal weight:    0.0770
   chunk 27 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.5936

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

Flipped N/Q/H residues before XYZ refinement:
A 467 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.108210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.082868 restraints weight = 9321.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.085274 restraints weight = 6059.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.086850 restraints weight = 4636.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6075  Z= 0.094
  Angle     :  0.498   7.937   8227  Z= 0.254
  Chirality :  0.042   0.158    915
  Planarity :  0.003   0.049   1071
  Dihedral  :  3.745  20.520    816
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.29 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.31), residues: 739
  helix:  1.62 (0.36), residues: 232
  sheet: -0.77 (0.43), residues: 124
  loop : -1.02 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 776 
 HIS   0.001   0.000   HIS A 808 
 PHE   0.029   0.001   PHE A 197 
 TYR   0.008   0.001   TYR A 746 
 ARG   0.003   0.000   ARG A 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02917 (  201)
  hydrogen bonds       : angle       4.01595 (  570)
  covalent geometry    : bond        0.00222 ( 6075)
  covalent geometry    : angle       0.49778 ( 8227)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3301.68 seconds
wall clock time: 60 minutes 31.21 seconds (3631.21 seconds total)