Starting phenix.real_space_refine
on Fri Jul 25 12:05:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8by6_16321/07_2025/8by6_16321.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8by6_16321/07_2025/8by6_16321.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8by6_16321/07_2025/8by6_16321.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8by6_16321/07_2025/8by6_16321.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8by6_16321/07_2025/8by6_16321.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8by6_16321/07_2025/8by6_16321.cif"
  }
  resolution = 3.19
  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=   0.012
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      44      5.16       5
     C    4842      2.51       5
     N    1307      2.21       5
     O    1405      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 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: 7601
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 748, 6120
          Classifications: {'peptide': 748}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 707}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1237
          Classifications: {'peptide': 152}
          Link IDs: {'TRANS': 151}
    Chain: "C"
      Number of atoms: 192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 192
          Classifications: {'peptide': 23}
          Link IDs: {'TRANS': 22}
    Chain: "B"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'GTG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.26, per 1000 atoms: 0.69
  Number of scatterers: 7601
  At special positions: 0
  Unit cell: (103.375, 91.797, 113.299, 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)
     S      44     16.00
     P       3     15.00
     O    1405      8.00
     N    1307      7.00
     C    4842      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: 2.18
  Conformation dependent library (CDL) restraints added in 910.5 milliseconds
  

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1778

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 1 sheets defined
      72.7% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 38
      removed outlier: 3.921A  pdb=" N   VAL A  38 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 60
    Processing helix  chain 'A' and resid 61 through 63
      No H-bonds generated for 'chain 'A' and resid 61 through 63'
    Processing helix  chain 'A' and resid 64 through 79
    Processing helix  chain 'A' and resid 82 through 95
    Processing helix  chain 'A' and resid 97 through 118
    Processing helix  chain 'A' and resid 121 through 137
      removed outlier: 4.077A  pdb=" N   ASN A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   CYS A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 155
      removed outlier: 3.515A  pdb=" N   MET A 145 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 158
      No H-bonds generated for 'chain 'A' and resid 156 through 158'
    Processing helix  chain 'A' and resid 162 through 205
      removed outlier: 3.782A  pdb=" N   ARG A 166 " --> pdb=" O   PRO A 162 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 6.307A  pdb=" N   LYS A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   GLU A 183 " --> pdb=" O   TRP A 179 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   ALA A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   GLU A 191 " --> pdb=" O   LYS A 187 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ARG A 205 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 215
      removed outlier: 3.507A  pdb=" N   LEU A 214 " --> pdb=" O   HIS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 242
    Processing helix  chain 'A' and resid 251 through 255
    Processing helix  chain 'A' and resid 256 through 262
      removed outlier: 3.578A  pdb=" N   GLU A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 297
    Processing helix  chain 'A' and resid 308 through 325
      removed outlier: 3.540A  pdb=" N   PHE A 312 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 338
    Processing helix  chain 'A' and resid 346 through 361
    Processing helix  chain 'A' and resid 368 through 383
      removed outlier: 3.588A  pdb=" N   TYR A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 401
    Processing helix  chain 'A' and resid 402 through 405
    Processing helix  chain 'A' and resid 406 through 424
    Processing helix  chain 'A' and resid 429 through 433
    Processing helix  chain 'A' and resid 434 through 439
      removed outlier: 4.296A  pdb=" N   SER A 438 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLN A 439 " --> pdb=" O   ASP A 435 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 434 through 439'
    Processing helix  chain 'A' and resid 443 through 459
    Processing helix  chain 'A' and resid 461 through 467
      removed outlier: 3.582A  pdb=" N   ILE A 465 " --> pdb=" O   TYR A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 477
      removed outlier: 4.547A  pdb=" N   ALA A 475 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 510
    Processing helix  chain 'A' and resid 513 through 522
    Processing helix  chain 'A' and resid 540 through 555
    Processing helix  chain 'A' and resid 558 through 569
    Processing helix  chain 'A' and resid 569 through 577
    Processing helix  chain 'A' and resid 579 through 594
    Processing helix  chain 'A' and resid 597 through 611
    Processing helix  chain 'A' and resid 615 through 624
      removed outlier: 3.533A  pdb=" N   PHE A 624 " --> pdb=" O   ALA A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 629
    Processing helix  chain 'A' and resid 634 through 676
      removed outlier: 3.977A  pdb=" N   TRP A 638 " --> pdb=" O   ARG A 634 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ASP A 676 " --> pdb=" O   ARG A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 732
    Processing helix  chain 'A' and resid 737 through 754
    Processing helix  chain 'A' and resid 754 through 769
      removed outlier: 4.961A  pdb=" N   GLN A 760 " --> pdb=" O   GLN A 756 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   TYR A 761 " --> pdb=" O   ILE A 757 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   VAL A 763 " --> pdb=" O   GLN A 759 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   THR A 764 " --> pdb=" O   GLN A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 789
      removed outlier: 4.057A  pdb=" N   VAL A 781 " --> pdb=" O   HIS A 777 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   PHE A 782 " --> pdb=" O   ILE A 778 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLN A 789 " --> pdb=" O   PHE A 785 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 11
    Processing helix  chain 'B' and resid 28 through 39
      removed outlier: 3.728A  pdb=" N   LYS B  38 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 62
      removed outlier: 3.704A  pdb=" N   ILE B  56 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 101
      removed outlier: 3.566A  pdb=" N   ALA B  94 " --> pdb=" O   SER B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 139
    Processing helix  chain 'B' and resid 143 through 147
    Processing helix  chain 'B' and resid 150 through 155
      removed outlier: 3.790A  pdb=" N   GLN B 154 " --> pdb=" O   GLY B 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 574 through 594
    Processing sheet with id=AA1, first strand: chain 'B' and resid 66 through 73
      removed outlier: 5.259A  pdb=" N   ILE B  66 " --> pdb=" O   GLU B  87 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   GLU B  87 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LYS B  68 " --> pdb=" O   PHE B  85 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   PHE B  85 " --> pdb=" O   LYS B  68 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   ILE B  70 " --> pdb=" O   PHE B  83 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   PHE B  83 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   GLY B  72 " --> pdb=" O   CYS B  81 " (cutoff:3.500A)

    458 hydrogen bonds defined for protein.
    1326 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: 2.13

  Time building geometry restraints manager: 2.53 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1330
        1.32 -     1.44: 2027
        1.44 -     1.57: 4352
        1.57 -     1.69: 6
        1.69 -     1.81: 66
  Bond restraints: 7781
  Sorted by residual:
  bond pdb=" C5A GTG B 201 "
       pdb=" C6A GTG B 201 "
    ideal  model  delta    sigma   weight residual
    1.427  1.330  0.097 2.00e-02 2.50e+03 2.35e+01
  bond pdb=" C5B GTG B 201 "
       pdb=" C6B GTG B 201 "
    ideal  model  delta    sigma   weight residual
    1.424  1.331  0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" C1D GTG B 201 "
       pdb=" O4D GTG B 201 "
    ideal  model  delta    sigma   weight residual
    1.383  1.466 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" C1E GTG B 201 "
       pdb=" O4E GTG B 201 "
    ideal  model  delta    sigma   weight residual
    1.392  1.473 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" C   PRO A 470 "
       pdb=" O   PRO A 470 "
    ideal  model  delta    sigma   weight residual
    1.240  1.204  0.036 1.12e-02 7.97e+03 1.03e+01
  ... (remaining 7776 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 10236
        1.99 -     3.98: 250
        3.98 -     5.98: 34
        5.98 -     7.97: 10
        7.97 -     9.96: 4
  Bond angle restraints: 10534
  Sorted by residual:
  angle pdb=" CA  ASP A  29 "
        pdb=" CB  ASP A  29 "
        pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  118.25   -5.65 1.00e+00 1.00e+00 3.19e+01
  angle pdb=" C   GLU A  26 "
        pdb=" CA  GLU A  26 "
        pdb=" CB  GLU A  26 "
      ideal   model   delta    sigma   weight residual
     110.96  117.98   -7.02 1.54e+00 4.22e-01 2.08e+01
  angle pdb=" C   ASP A  29 "
        pdb=" CA  ASP A  29 "
        pdb=" CB  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     110.81  117.87   -7.06 1.60e+00 3.91e-01 1.95e+01
  angle pdb=" N   GLU A  26 "
        pdb=" CA  GLU A  26 "
        pdb=" C   GLU A  26 "
      ideal   model   delta    sigma   weight residual
     110.97  106.44    4.53 1.09e+00 8.42e-01 1.73e+01
  angle pdb=" C   SER A  33 "
        pdb=" N   LEU A  34 "
        pdb=" CA  LEU A  34 "
      ideal   model   delta    sigma   weight residual
     120.54  125.16   -4.62 1.35e+00 5.49e-01 1.17e+01
  ... (remaining 10529 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.94: 4294
       26.94 -    53.87: 396
       53.87 -    80.81: 47
       80.81 -   107.74: 5
      107.74 -   134.68: 1
  Dihedral angle restraints: 4743
    sinusoidal: 2013
      harmonic: 2730
  Sorted by residual:
  dihedral pdb=" O5D GTG B 201 "
           pdb=" O3A GTG B 201 "
           pdb=" PA  GTG B 201 "
           pdb=" PB  GTG B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -105.71   28.97 -134.68     1      3.00e+01 1.11e-03 1.82e+01
  dihedral pdb=" CA  ASP B 114 "
           pdb=" CB  ASP B 114 "
           pdb=" CG  ASP B 114 "
           pdb=" OD1 ASP B 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.39   58.39     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CA  ASP A 369 "
           pdb=" CB  ASP A 369 "
           pdb=" CG  ASP A 369 "
           pdb=" OD1 ASP A 369 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.27   58.27     1      2.00e+01 2.50e-03 1.14e+01
  ... (remaining 4740 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 945
       0.046 -    0.092: 147
       0.092 -    0.138: 45
       0.138 -    0.183: 4
       0.183 -    0.229: 3
  Chirality restraints: 1144
  Sorted by residual:
  chirality pdb=" C4E GTG B 201 "
            pdb=" C3E GTG B 201 "
            pdb=" C5E GTG B 201 "
            pdb=" O4E GTG B 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.78    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" C4D GTG B 201 "
            pdb=" C3D GTG B 201 "
            pdb=" C5D GTG B 201 "
            pdb=" O4D GTG B 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.75    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  THR A  88 "
            pdb=" N   THR A  88 "
            pdb=" C   THR A  88 "
            pdb=" CB  THR A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.71   -0.18 2.00e-01 2.50e+01 8.51e-01
  ... (remaining 1141 not shown)

  Planarity restraints: 1345
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  61 "   -0.050 5.00e-02 4.00e+02   7.36e-02 8.66e+00
        pdb=" N   PRO A  62 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A  62 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A  62 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 258 "    0.011 2.00e-02 2.50e+03   2.23e-02 4.99e+00
        pdb=" C   SER A 258 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   SER A 258 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ILE A 259 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 461 "    0.021 2.00e-02 2.50e+03   1.32e-02 3.50e+00
        pdb=" CG  TYR A 461 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 461 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 461 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 461 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 461 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 461 "    0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A 461 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1342 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.62: 84
        2.62 -     3.19: 6883
        3.19 -     3.76: 12195
        3.76 -     4.33: 16291
        4.33 -     4.90: 27567
  Nonbonded interactions: 63020
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  32 "
            pdb=" CG  LYS B   7 "
     model   vdw
     2.044 3.440
  nonbonded pdb=" O   SER B  63 "
            pdb=" OG  SER B  63 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OD2 ASP A 167 "
            pdb=" NH2 ARG A 206 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" OH  TYR B  20 "
            pdb=" O2D GTG B 201 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   ILE A 414 "
            pdb=" OG  SER A 418 "
     model   vdw
     2.282 3.040
  ... (remaining 63015 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 individual isotropic
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:             1.870
  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:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.450
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
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      :  0.005   0.097   7781  Z= 0.264
  Angle     :  0.719   9.959  10534  Z= 0.394
  Chirality :  0.040   0.229   1144
  Planarity :  0.004   0.074   1345
  Dihedral  : 18.826 134.677   2965
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 27.73 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.38 (0.28), residues: 913
  helix:  2.33 (0.22), residues: 594
  sheet: -1.19 (1.23), residues: 11
  loop :  0.25 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 416 
 HIS   0.013   0.001   HIS A 570 
 PHE   0.008   0.001   PHE A 473 
 TYR   0.029   0.001   TYR A 461 
 ARG   0.004   0.000   ARG A 464 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11732 (  458)
  hydrogen bonds       : angle       4.73119 ( 1326)
  covalent geometry    : bond        0.00496 ( 7781)
  covalent geometry    : angle       0.71913 (10534)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7472 (p0)
REVERT: A  648 MET cc_start: 0.8727 (tpp) cc_final: 0.8514 (tpt)
  outliers start: 24
  outliers final: 11
  residues processed: 147
  average time/residue: 0.2163
  time to fit residues: 42.3868
Evaluate side-chains
  99 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  701 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 46 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 82 optimal weight:    0.5980
   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 111 GLN
A 245 GLN
A 317 ASN
A 561 HIS
A 753 GLN
B  55 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.078467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.058581 restraints weight = 18983.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 3.30
r_work: 0.2671 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7781  Z= 0.138
  Angle     :  0.558   7.381  10534  Z= 0.286
  Chirality :  0.039   0.163   1144
  Planarity :  0.004   0.045   1345
  Dihedral  :  7.198 128.526   1082
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 26.17 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.74 (0.28), residues: 913
  helix:  2.58 (0.21), residues: 610
  sheet: -0.65 (1.25), residues: 11
  loop :  0.29 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 168 
 HIS   0.007   0.001   HIS A 570 
 PHE   0.019   0.001   PHE B  25 
 TYR   0.014   0.001   TYR A  86 
 ARG   0.005   0.000   ARG B 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  458)
  hydrogen bonds       : angle       3.78144 ( 1326)
  covalent geometry    : bond        0.00328 ( 7781)
  covalent geometry    : angle       0.55797 (10534)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7787 (p0)
REVERT: A  114 GLU cc_start: 0.9232 (tt0) cc_final: 0.8773 (tm-30)
REVERT: A  133 ASP cc_start: 0.9582 (t70) cc_final: 0.9211 (t70)
REVERT: A  220 ASP cc_start: 0.8702 (p0) cc_final: 0.8418 (p0)
REVERT: A  316 GLU cc_start: 0.8383 (tp30) cc_final: 0.8168 (tp30)
REVERT: B   46 ASN cc_start: 0.9172 (t0) cc_final: 0.8879 (t0)
REVERT: B   54 GLU cc_start: 0.9165 (mp0) cc_final: 0.8886 (mp0)
REVERT: B   81 CYS cc_start: 0.8715 (t) cc_final: 0.8179 (m)
REVERT: B  116 ASP cc_start: 0.8792 (t0) cc_final: 0.7946 (t70)
REVERT: B  121 GLU cc_start: 0.9305 (mm-30) cc_final: 0.9011 (tp30)
  outliers start: 22
  outliers final: 11
  residues processed: 101
  average time/residue: 0.2105
  time to fit residues: 28.8783
Evaluate side-chains
  96 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain C residue  585 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 27 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   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 540 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 = 0.3274 r_free = 0.3274 target = 0.077784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.058050 restraints weight = 19333.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 3.28
r_work: 0.2670 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7781  Z= 0.128
  Angle     :  0.512   7.432  10534  Z= 0.261
  Chirality :  0.038   0.166   1144
  Planarity :  0.004   0.046   1345
  Dihedral  :  6.641 123.313   1073
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 26.41 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  2.89 (0.28), residues: 913
  helix:  2.73 (0.21), residues: 608
  sheet: -0.63 (1.25), residues: 11
  loop :  0.30 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 638 
 HIS   0.004   0.001   HIS A 570 
 PHE   0.014   0.001   PHE A 569 
 TYR   0.016   0.001   TYR A  86 
 ARG   0.005   0.000   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03555 (  458)
  hydrogen bonds       : angle       3.62243 ( 1326)
  covalent geometry    : bond        0.00307 ( 7781)
  covalent geometry    : angle       0.51213 (10534)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.9145 (tpp) cc_final: 0.8817 (tpp)
REVERT: A  114 GLU cc_start: 0.9221 (tt0) cc_final: 0.8781 (tm-30)
REVERT: A  133 ASP cc_start: 0.9538 (t70) cc_final: 0.9198 (t70)
REVERT: A  200 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8320 (tm-30)
REVERT: A  220 ASP cc_start: 0.8789 (p0) cc_final: 0.8438 (p0)
REVERT: A  316 GLU cc_start: 0.8576 (tp30) cc_final: 0.8330 (tp30)
REVERT: B   25 PHE cc_start: 0.9264 (t80) cc_final: 0.8960 (t80)
REVERT: B   31 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8804 (tm-30)
REVERT: B   46 ASN cc_start: 0.9210 (t0) cc_final: 0.8887 (t0)
REVERT: B   54 GLU cc_start: 0.9146 (mp0) cc_final: 0.8868 (mp0)
REVERT: B   81 CYS cc_start: 0.8783 (t) cc_final: 0.8120 (m)
REVERT: B  110 ILE cc_start: 0.9371 (mm) cc_final: 0.9132 (mm)
REVERT: B  116 ASP cc_start: 0.8832 (t0) cc_final: 0.8523 (t70)
  outliers start: 25
  outliers final: 12
  residues processed: 108
  average time/residue: 0.2365
  time to fit residues: 33.8295
Evaluate side-chains
  90 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain B residue   76 MET
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain C residue  585 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    0.0270
   chunk 60 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0370
   chunk 90 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 706 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.078371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.057955 restraints weight = 19227.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 3.40
r_work: 0.2672 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7781  Z= 0.112
  Angle     :  0.495   7.419  10534  Z= 0.252
  Chirality :  0.037   0.154   1144
  Planarity :  0.004   0.046   1345
  Dihedral  :  6.275 119.342   1069
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 25.69 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  3.01 (0.28), residues: 913
  helix:  2.78 (0.21), residues: 610
  sheet: -0.92 (1.10), residues: 16
  loop :  0.49 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 416 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.014   0.001   PHE A 569 
 TYR   0.009   0.001   TYR A 461 
 ARG   0.004   0.000   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03303 (  458)
  hydrogen bonds       : angle       3.54493 ( 1326)
  covalent geometry    : bond        0.00268 ( 7781)
  covalent geometry    : angle       0.49545 (10534)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 THR cc_start: 0.9251 (m) cc_final: 0.8926 (t)
REVERT: A  108 MET cc_start: 0.9151 (tpp) cc_final: 0.8951 (tpp)
REVERT: A  114 GLU cc_start: 0.9209 (tt0) cc_final: 0.8840 (tm-30)
REVERT: A  133 ASP cc_start: 0.9490 (t70) cc_final: 0.8821 (t70)
REVERT: A  200 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8309 (tm-30)
REVERT: A  220 ASP cc_start: 0.8840 (p0) cc_final: 0.8444 (p0)
REVERT: A  261 CYS cc_start: 0.9281 (t) cc_final: 0.9055 (p)
REVERT: A  316 GLU cc_start: 0.8605 (tp30) cc_final: 0.8339 (tp30)
REVERT: B   46 ASN cc_start: 0.9198 (t0) cc_final: 0.8830 (t0)
REVERT: B   54 GLU cc_start: 0.9143 (mp0) cc_final: 0.8847 (mp0)
REVERT: B   81 CYS cc_start: 0.8773 (t) cc_final: 0.8086 (m)
REVERT: B  110 ILE cc_start: 0.9370 (mm) cc_final: 0.9126 (mm)
REVERT: B  116 ASP cc_start: 0.8847 (t0) cc_final: 0.8565 (t70)
REVERT: B  129 ARG cc_start: 0.8881 (ptm-80) cc_final: 0.8645 (ttp80)
  outliers start: 24
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1987
  time to fit residues: 27.9081
Evaluate side-chains
  89 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  345 ILE
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain C residue  585 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 9 optimal weight:    0.2980
   chunk 69 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0060
   chunk 38 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 85 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
** A 540 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 = 0.3289 r_free = 0.3289 target = 0.078460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.058012 restraints weight = 19316.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 3.42
r_work: 0.2679 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7781  Z= 0.109
  Angle     :  0.496   8.937  10534  Z= 0.251
  Chirality :  0.037   0.148   1144
  Planarity :  0.004   0.045   1345
  Dihedral  :  6.156 114.914   1069
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 26.53 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  3.05 (0.28), residues: 913
  helix:  2.79 (0.21), residues: 610
  sheet: -0.85 (1.09), residues: 16
  loop :  0.53 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 638 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.013   0.001   PHE A 569 
 TYR   0.009   0.001   TYR A 461 
 ARG   0.003   0.000   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03210 (  458)
  hydrogen bonds       : angle       3.53859 ( 1326)
  covalent geometry    : bond        0.00260 ( 7781)
  covalent geometry    : angle       0.49597 (10534)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.9135 (tpp) cc_final: 0.8910 (tpp)
REVERT: A  114 GLU cc_start: 0.9206 (tt0) cc_final: 0.8842 (tm-30)
REVERT: A  133 ASP cc_start: 0.9450 (t70) cc_final: 0.9110 (t70)
REVERT: A  200 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8304 (tm-30)
REVERT: A  220 ASP cc_start: 0.8865 (p0) cc_final: 0.8443 (p0)
REVERT: A  261 CYS cc_start: 0.9273 (t) cc_final: 0.9054 (p)
REVERT: A  316 GLU cc_start: 0.8643 (tp30) cc_final: 0.8371 (tp30)
REVERT: B   46 ASN cc_start: 0.9185 (t0) cc_final: 0.8719 (t0)
REVERT: B   54 GLU cc_start: 0.9142 (mp0) cc_final: 0.8813 (mp0)
REVERT: B   81 CYS cc_start: 0.8798 (t) cc_final: 0.8150 (m)
REVERT: B  116 ASP cc_start: 0.8855 (t0) cc_final: 0.8483 (t70)
REVERT: B  129 ARG cc_start: 0.8864 (ptm-80) cc_final: 0.8587 (ttp80)
  outliers start: 20
  outliers final: 12
  residues processed: 100
  average time/residue: 0.2095
  time to fit residues: 28.6029
Evaluate side-chains
  90 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain C residue  585 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 88 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 225 GLN
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.077652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.057032 restraints weight = 19657.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 3.45
r_work: 0.2654 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7781  Z= 0.129
  Angle     :  0.507   8.008  10534  Z= 0.255
  Chirality :  0.038   0.146   1144
  Planarity :  0.004   0.044   1345
  Dihedral  :  6.089 111.190   1069
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 26.05 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  3.09 (0.28), residues: 913
  helix:  2.81 (0.21), residues: 610
  sheet: -0.29 (1.29), residues: 11
  loop :  0.54 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 638 
 HIS   0.003   0.001   HIS A 319 
 PHE   0.012   0.001   PHE A 569 
 TYR   0.015   0.001   TYR A  86 
 ARG   0.003   0.000   ARG A 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03308 (  458)
  hydrogen bonds       : angle       3.49831 ( 1326)
  covalent geometry    : bond        0.00314 ( 7781)
  covalent geometry    : angle       0.50667 (10534)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.9154 (tpp) cc_final: 0.8874 (tpp)
REVERT: A  114 GLU cc_start: 0.9226 (tt0) cc_final: 0.8861 (tm-30)
REVERT: A  133 ASP cc_start: 0.9475 (t70) cc_final: 0.9065 (t70)
REVERT: A  200 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8292 (tm-30)
REVERT: A  220 ASP cc_start: 0.8874 (p0) cc_final: 0.8463 (p0)
REVERT: A  225 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.8212 (mp-120)
REVERT: A  261 CYS cc_start: 0.9290 (t) cc_final: 0.9084 (p)
REVERT: A  316 GLU cc_start: 0.8703 (tp30) cc_final: 0.8430 (tp30)
REVERT: B   10 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.7970 (ttm170)
REVERT: B   46 ASN cc_start: 0.9193 (t0) cc_final: 0.8711 (t0)
REVERT: B   54 GLU cc_start: 0.9157 (mp0) cc_final: 0.8820 (mp0)
REVERT: B   81 CYS cc_start: 0.8871 (t) cc_final: 0.8113 (m)
REVERT: B  116 ASP cc_start: 0.8838 (t0) cc_final: 0.8568 (t70)
  outliers start: 23
  outliers final: 13
  residues processed: 102
  average time/residue: 0.2153
  time to fit residues: 30.0231
Evaluate side-chains
  94 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   32 GLN
Chi-restraints excluded: chain C residue  585 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 82 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0170
   chunk 36 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 GLN ** 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 = 0.3282 r_free = 0.3282 target = 0.078144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.057587 restraints weight = 19521.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 3.45
r_work: 0.2674 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7781  Z= 0.116
  Angle     :  0.527   7.732  10534  Z= 0.264
  Chirality :  0.038   0.133   1144
  Planarity :  0.004   0.043   1345
  Dihedral  :  5.970 109.648   1069
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 27.13 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  3.08 (0.28), residues: 913
  helix:  2.79 (0.21), residues: 610
  sheet: -0.17 (1.33), residues: 11
  loop :  0.54 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 638 
 HIS   0.003   0.001   HIS A 754 
 PHE   0.012   0.001   PHE A 569 
 TYR   0.012   0.001   TYR A  86 
 ARG   0.006   0.000   ARG A 668 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03210 (  458)
  hydrogen bonds       : angle       3.48343 ( 1326)
  covalent geometry    : bond        0.00284 ( 7781)
  covalent geometry    : angle       0.52677 (10534)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.9151 (tpp) cc_final: 0.8880 (tpp)
REVERT: A  114 GLU cc_start: 0.9237 (tt0) cc_final: 0.8874 (tm-30)
REVERT: A  133 ASP cc_start: 0.9458 (t70) cc_final: 0.9003 (t70)
REVERT: A  200 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8291 (tm-30)
REVERT: A  207 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8769 (mp10)
REVERT: A  220 ASP cc_start: 0.8873 (p0) cc_final: 0.8449 (p0)
REVERT: A  316 GLU cc_start: 0.8696 (tp30) cc_final: 0.8428 (tp30)
REVERT: B   46 ASN cc_start: 0.9173 (t0) cc_final: 0.8685 (t0)
REVERT: B   54 GLU cc_start: 0.9134 (mp0) cc_final: 0.8799 (mp0)
REVERT: B   81 CYS cc_start: 0.8869 (t) cc_final: 0.8096 (m)
REVERT: B  116 ASP cc_start: 0.8820 (t0) cc_final: 0.8564 (t70)
REVERT: B  129 ARG cc_start: 0.8844 (ptm-80) cc_final: 0.8554 (ttp80)
  outliers start: 16
  outliers final: 11
  residues processed: 97
  average time/residue: 0.2352
  time to fit residues: 30.7245
Evaluate side-chains
  91 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  345 ILE
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain C residue  585 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 88 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0170
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.6020

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

Flipped N/Q/H residues before XYZ refinement:
** A 540 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 = 0.3285 r_free = 0.3285 target = 0.078278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.057951 restraints weight = 19584.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 3.41
r_work: 0.2680 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7781  Z= 0.115
  Angle     :  0.520   7.742  10534  Z= 0.261
  Chirality :  0.038   0.129   1144
  Planarity :  0.004   0.043   1345
  Dihedral  :  5.828 105.521   1069
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 27.25 %
    Favored  : 70.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  3.09 (0.28), residues: 913
  helix:  2.78 (0.21), residues: 610
  sheet: -0.11 (1.33), residues: 11
  loop :  0.59 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 638 
 HIS   0.003   0.001   HIS A 319 
 PHE   0.012   0.001   PHE A 569 
 TYR   0.011   0.001   TYR A  86 
 ARG   0.007   0.000   ARG B  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03162 (  458)
  hydrogen bonds       : angle       3.45671 ( 1326)
  covalent geometry    : bond        0.00281 ( 7781)
  covalent geometry    : angle       0.51960 (10534)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.9162 (tpp) cc_final: 0.8778 (tpp)
REVERT: A  114 GLU cc_start: 0.9222 (tt0) cc_final: 0.8874 (tm-30)
REVERT: A  133 ASP cc_start: 0.9442 (t70) cc_final: 0.9019 (t70)
REVERT: A  200 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8269 (tm-30)
REVERT: A  207 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8808 (mp10)
REVERT: A  220 ASP cc_start: 0.8865 (p0) cc_final: 0.8462 (p0)
REVERT: A  316 GLU cc_start: 0.8723 (tp30) cc_final: 0.8471 (tp30)
REVERT: B   25 PHE cc_start: 0.9084 (t80) cc_final: 0.8752 (t80)
REVERT: B   31 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8760 (tm-30)
REVERT: B   46 ASN cc_start: 0.9148 (t0) cc_final: 0.8644 (t0)
REVERT: B   54 GLU cc_start: 0.9119 (mp0) cc_final: 0.8789 (mp0)
REVERT: B   81 CYS cc_start: 0.8922 (t) cc_final: 0.8135 (m)
REVERT: B  116 ASP cc_start: 0.8821 (t0) cc_final: 0.8579 (t70)
REVERT: B  129 ARG cc_start: 0.8847 (ptm-80) cc_final: 0.8515 (ttp80)
REVERT: B  141 ASP cc_start: 0.9138 (t0) cc_final: 0.8925 (p0)
  outliers start: 17
  outliers final: 12
  residues processed: 98
  average time/residue: 0.2162
  time to fit residues: 28.5811
Evaluate side-chains
  96 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain C residue  585 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0170
   chunk 30 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   chunk 9 optimal weight:    0.2980
   chunk 88 optimal weight:   10.0000
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
** A 540 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 = 0.3282 r_free = 0.3282 target = 0.077829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.057531 restraints weight = 19890.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 3.45
r_work: 0.2666 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7781  Z= 0.121
  Angle     :  0.527   8.039  10534  Z= 0.265
  Chirality :  0.038   0.136   1144
  Planarity :  0.004   0.043   1345
  Dihedral  :  5.566 101.728   1066
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 27.61 %
    Favored  : 70.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  3.20 (0.28), residues: 913
  helix:  2.82 (0.21), residues: 604
  sheet: -0.06 (1.34), residues: 11
  loop :  0.78 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 638 
 HIS   0.003   0.001   HIS A 319 
 PHE   0.011   0.001   PHE A 569 
 TYR   0.014   0.001   TYR A  86 
 ARG   0.009   0.000   ARG A 668 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03174 (  458)
  hydrogen bonds       : angle       3.47073 ( 1326)
  covalent geometry    : bond        0.00293 ( 7781)
  covalent geometry    : angle       0.52693 (10534)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.9158 (tpp) cc_final: 0.8762 (tpp)
REVERT: A  114 GLU cc_start: 0.9234 (tt0) cc_final: 0.8878 (tm-30)
REVERT: A  133 ASP cc_start: 0.9433 (t70) cc_final: 0.9020 (t70)
REVERT: A  200 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8275 (tm-30)
REVERT: A  207 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8786 (mp10)
REVERT: A  220 ASP cc_start: 0.8881 (p0) cc_final: 0.8464 (p0)
REVERT: A  316 GLU cc_start: 0.8734 (tp30) cc_final: 0.8483 (tp30)
REVERT: B   25 PHE cc_start: 0.9064 (t80) cc_final: 0.8746 (t80)
REVERT: B   31 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8695 (tm-30)
REVERT: B   46 ASN cc_start: 0.9159 (t0) cc_final: 0.8649 (t0)
REVERT: B   54 GLU cc_start: 0.9145 (mp0) cc_final: 0.8809 (mp0)
REVERT: B   81 CYS cc_start: 0.8926 (t) cc_final: 0.8103 (m)
REVERT: B  116 ASP cc_start: 0.8831 (t0) cc_final: 0.8597 (t70)
REVERT: B  141 ASP cc_start: 0.9165 (t0) cc_final: 0.8940 (p0)
  outliers start: 16
  outliers final: 12
  residues processed: 94
  average time/residue: 0.2236
  time to fit residues: 28.2570
Evaluate side-chains
  94 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain C residue  585 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 31 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 88 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 350 HIS
** A 540 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 = 0.3260 r_free = 0.3260 target = 0.076777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.056319 restraints weight = 19973.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 3.46
r_work: 0.2639 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7781  Z= 0.150
  Angle     :  0.562  10.508  10534  Z= 0.281
  Chirality :  0.039   0.148   1144
  Planarity :  0.004   0.042   1345
  Dihedral  :  5.563 100.435   1066
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 27.73 %
    Favored  : 70.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  3.06 (0.29), residues: 913
  helix:  2.72 (0.21), residues: 610
  sheet:  0.05 (1.36), residues: 11
  loop :  0.68 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A 754 
 PHE   0.011   0.001   PHE A 569 
 TYR   0.016   0.001   TYR A  86 
 ARG   0.012   0.001   ARG A 668 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03319 (  458)
  hydrogen bonds       : angle       3.50483 ( 1326)
  covalent geometry    : bond        0.00368 ( 7781)
  covalent geometry    : angle       0.56242 (10534)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.9186 (tpp) cc_final: 0.8782 (tpp)
REVERT: A  114 GLU cc_start: 0.9242 (tt0) cc_final: 0.8886 (tm-30)
REVERT: A  133 ASP cc_start: 0.9446 (t70) cc_final: 0.9042 (t70)
REVERT: A  200 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8301 (tm-30)
REVERT: A  207 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8776 (mp10)
REVERT: A  220 ASP cc_start: 0.8907 (p0) cc_final: 0.8489 (p0)
REVERT: A  316 GLU cc_start: 0.8772 (tp30) cc_final: 0.8518 (tp30)
REVERT: B   25 PHE cc_start: 0.9070 (t80) cc_final: 0.8810 (t80)
REVERT: B   31 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8730 (tm-30)
REVERT: B   46 ASN cc_start: 0.9138 (t0) cc_final: 0.8630 (t0)
REVERT: B   54 GLU cc_start: 0.9156 (mp0) cc_final: 0.8831 (mp0)
REVERT: B   81 CYS cc_start: 0.8975 (t) cc_final: 0.8089 (m)
REVERT: B  129 ARG cc_start: 0.8828 (ptm-80) cc_final: 0.8618 (ttp80)
REVERT: B  141 ASP cc_start: 0.9131 (t0) cc_final: 0.8862 (p0)
  outliers start: 16
  outliers final: 13
  residues processed: 99
  average time/residue: 0.2460
  time to fit residues: 31.8221
Evaluate side-chains
  97 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain C residue  585 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0970
   chunk 65 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0030
   chunk 42 optimal weight:    0.0370
   overall best weight:    0.4066

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

Flipped N/Q/H residues before XYZ refinement:
A 350 HIS
** A 540 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 = 0.3293 r_free = 0.3293 target = 0.078315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.058034 restraints weight = 19729.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 3.46
r_work: 0.2678 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7781  Z= 0.114
  Angle     :  0.565  10.163  10534  Z= 0.282
  Chirality :  0.038   0.172   1144
  Planarity :  0.004   0.042   1345
  Dihedral  :  5.482  97.559   1066
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 28.09 %
    Favored  : 69.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  3.18 (0.29), residues: 913
  helix:  2.75 (0.21), residues: 610
  sheet:  0.08 (1.42), residues: 11
  loop :  0.87 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 638 
 HIS   0.003   0.001   HIS A 319 
 PHE   0.011   0.001   PHE A 569 
 TYR   0.012   0.001   TYR A  86 
 ARG   0.007   0.000   ARG B  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03126 (  458)
  hydrogen bonds       : angle       3.47172 ( 1326)
  covalent geometry    : bond        0.00280 ( 7781)
  covalent geometry    : angle       0.56532 (10534)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3571.81 seconds
wall clock time: 62 minutes 13.13 seconds (3733.13 seconds total)