Starting phenix.real_space_refine
on Sat May 10 01:51:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rfb_19117/05_2025/8rfb_19117_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rfb_19117/05_2025/8rfb_19117.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rfb_19117/05_2025/8rfb_19117.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rfb_19117/05_2025/8rfb_19117.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rfb_19117/05_2025/8rfb_19117_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rfb_19117/05_2025/8rfb_19117_neut.cif"
  }
  resolution = 4.01
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    2979      2.51       5
     N     765      2.21       5
     O     864      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4632
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4632
          Classifications: {'peptide': 597}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 32, 'TRANS': 564}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 221
          Unresolved non-hydrogen dihedrals: 151
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 15, 'ASN:plan1': 1, 'ASP:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 118
  Time building chain proxies: 3.19, per 1000 atoms: 0.69
  Number of scatterers: 4632
  At special positions: 0
  Unit cell: (69.39, 74.9412, 103.622, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O     864      8.00
     N     765      7.00
     C    2979      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 507 " - pdb=" SG  CYS A 538 " distance=2.67

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.21
  Conformation dependent library (CDL) restraints added in 581.2 milliseconds
  

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1132

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 9 sheets defined
      22.9% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 149 through 152
    Processing helix  chain 'A' and resid 333 through 337
    Processing helix  chain 'A' and resid 436 through 440
    Processing helix  chain 'A' and resid 491 through 501
    Processing helix  chain 'A' and resid 516 through 522
      removed outlier: 3.816A  pdb=" N   HIS A 520 " --> pdb=" O   GLY A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 546
      removed outlier: 4.175A  pdb=" N   GLY A 531 " --> pdb=" O   LYS A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 551
      No H-bonds generated for 'chain 'A' and resid 549 through 551'
    Processing helix  chain 'A' and resid 561 through 572
    Processing helix  chain 'A' and resid 573 through 576
    Processing helix  chain 'A' and resid 587 through 593
    Processing helix  chain 'A' and resid 600 through 605
    Processing helix  chain 'A' and resid 613 through 624
    Processing helix  chain 'A' and resid 649 through 672
      removed outlier: 3.593A  pdb=" N   ILE A 653 " --> pdb=" O   PRO A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 711
    Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 117
      removed outlier: 6.584A  pdb=" N   LEU A 129 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 163
      removed outlier: 6.515A  pdb=" N   LYS A 173 " --> pdb=" O   ASP A 159 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   ILE A 161 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ALA A 171 " --> pdb=" O   ILE A 161 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   VAL A 163 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   TYR A 169 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   LYS A 188 " --> pdb=" O   MET A 195 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   MET A 195 " --> pdb=" O   LYS A 188 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 209
      removed outlier: 7.554A  pdb=" N   VAL A 202 " --> pdb=" O   GLN A 222 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   GLN A 222 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER A 204 " --> pdb=" O   THR A 220 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   CYS A 227 " --> pdb=" O   ARG A 223 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   HIS A 228 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   THR A 246 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL A 230 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 258
      removed outlier: 7.476A  pdb=" N   VAL A 277 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 305
      removed outlier: 5.882A  pdb=" N   ARG A 326 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   LEU A 339 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 354
      removed outlier: 6.958A  pdb=" N   PHE A 362 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU A 352 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   VAL A 360 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   MET A 354 " --> pdb=" O   HIS A 358 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   HIS A 358 " --> pdb=" O   MET A 354 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 395
      removed outlier: 3.524A  pdb=" N   CYS A 409 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   SER A 410 " --> pdb=" O   PRO A 414 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 445
      removed outlier: 6.257A  pdb=" N   LEU A 475 " --> pdb=" O   ALA A 505 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   CYS A 507 " --> pdb=" O   LEU A 475 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   HIS A 477 " --> pdb=" O   CYS A 507 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   LEU A 474 " --> pdb=" O   THR A 554 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   THR A 556 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   VAL A 476 " --> pdb=" O   THR A 556 " (cutoff:3.500A)
      removed outlier: 8.394A  pdb=" N   PHE A 558 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      removed outlier: 8.053A  pdb=" N   VAL A 478 " --> pdb=" O   PHE A 558 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   THR A 553 " --> pdb=" O   ALA A 578 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   THR A 580 " --> pdb=" O   THR A 553 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LEU A 555 " --> pdb=" O   THR A 580 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   GLU A 582 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   ALA A 557 " --> pdb=" O   GLU A 582 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 449

    193 hydrogen bonds defined for protein.
    528 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.48

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 881
        1.32 -     1.45: 1301
        1.45 -     1.57: 2530
        1.57 -     1.70: 3
        1.70 -     1.83: 34
  Bond restraints: 4749
  Sorted by residual:
  bond pdb=" CA  GLY A 513 "
       pdb=" C   GLY A 513 "
    ideal  model  delta    sigma   weight residual
    1.511  1.553 -0.042 1.03e-02 9.43e+03 1.67e+01
  bond pdb=" CA  ALA A 583 "
       pdb=" C   ALA A 583 "
    ideal  model  delta    sigma   weight residual
    1.534  1.496  0.038 9.50e-03 1.11e+04 1.58e+01
  bond pdb=" N   PRO A 584 "
       pdb=" CA  PRO A 584 "
    ideal  model  delta    sigma   weight residual
    1.466  1.418  0.047 1.19e-02 7.06e+03 1.58e+01
  bond pdb=" CB  HIS A 638 "
       pdb=" CG  HIS A 638 "
    ideal  model  delta    sigma   weight residual
    1.497  1.446  0.051 1.40e-02 5.10e+03 1.34e+01
  bond pdb=" C   ASN A 271 "
       pdb=" N   LYS A 272 "
    ideal  model  delta    sigma   weight residual
    1.333  1.278  0.054 1.50e-02 4.44e+03 1.32e+01
  ... (remaining 4744 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 5813
        2.65 -     5.29: 588
        5.29 -     7.94: 62
        7.94 -    10.59: 7
       10.59 -    13.24: 1
  Bond angle restraints: 6471
  Sorted by residual:
  angle pdb=" C   ASP A 249 "
        pdb=" N   PRO A 250 "
        pdb=" CA  PRO A 250 "
      ideal   model   delta    sigma   weight residual
     119.56  127.86   -8.30 1.02e+00 9.61e-01 6.62e+01
  angle pdb=" C   THR A 331 "
        pdb=" N   PRO A 332 "
        pdb=" CA  PRO A 332 "
      ideal   model   delta    sigma   weight residual
     119.56  127.40   -7.84 1.01e+00 9.80e-01 6.02e+01
  angle pdb=" C   ARG A 413 "
        pdb=" N   PRO A 414 "
        pdb=" CA  PRO A 414 "
      ideal   model   delta    sigma   weight residual
     119.66  125.07   -5.41 7.30e-01 1.88e+00 5.50e+01
  angle pdb=" C   PRO A 387 "
        pdb=" N   PRO A 388 "
        pdb=" CA  PRO A 388 "
      ideal   model   delta    sigma   weight residual
     119.56  126.87   -7.31 1.02e+00 9.61e-01 5.14e+01
  angle pdb=" N   ASN A 241 "
        pdb=" CA  ASN A 241 "
        pdb=" C   ASN A 241 "
      ideal   model   delta    sigma   weight residual
     107.98  121.22  -13.24 1.88e+00 2.83e-01 4.96e+01
  ... (remaining 6466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 2686
       17.98 -    35.96: 101
       35.96 -    53.95: 19
       53.95 -    71.93: 14
       71.93 -    89.91: 2
  Dihedral angle restraints: 2822
    sinusoidal: 1069
      harmonic: 1753
  Sorted by residual:
  dihedral pdb=" CA  ARG A 524 "
           pdb=" C   ARG A 524 "
           pdb=" N   LEU A 525 "
           pdb=" CA  LEU A 525 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.50  -20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  ASP A 713 "
           pdb=" CB  ASP A 713 "
           pdb=" CG  ASP A 713 "
           pdb=" OD1 ASP A 713 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.32   57.32     1      2.00e+01 2.50e-03 1.10e+01
  dihedral pdb=" CB  GLU A 276 "
           pdb=" CG  GLU A 276 "
           pdb=" CD  GLU A 276 "
           pdb=" OE1 GLU A 276 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.91  -89.91     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 2819 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 324
       0.056 -    0.112: 222
       0.112 -    0.168: 126
       0.168 -    0.224: 44
       0.224 -    0.280: 16
  Chirality restraints: 732
  Sorted by residual:
  chirality pdb=" CG  LEU A 589 "
            pdb=" CB  LEU A 589 "
            pdb=" CD1 LEU A 589 "
            pdb=" CD2 LEU A 589 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.87    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  ILE A 269 "
            pdb=" N   ILE A 269 "
            pdb=" C   ILE A 269 "
            pdb=" CB  ILE A 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  LEU A 515 "
            pdb=" N   LEU A 515 "
            pdb=" C   LEU A 515 "
            pdb=" CB  LEU A 515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.67e+00
  ... (remaining 729 not shown)

  Planarity restraints: 830
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 519 "   -0.048 2.00e-02 2.50e+03   2.78e-02 1.93e+01
        pdb=" CG  TRP A 519 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 519 "    0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 519 "    0.009 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 519 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 519 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 519 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 519 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 519 "    0.025 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 519 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 257 "   -0.041 2.00e-02 2.50e+03   2.39e-02 1.15e+01
        pdb=" CG  TYR A 257 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 257 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 257 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 257 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 257 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 257 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 257 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 421 "   -0.017 2.00e-02 2.50e+03   3.37e-02 1.14e+01
        pdb=" C   LYS A 421 "    0.058 2.00e-02 2.50e+03
        pdb=" O   LYS A 421 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   PHE A 422 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 827 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 240
        2.70 -     3.25: 4391
        3.25 -     3.80: 7328
        3.80 -     4.35: 9774
        4.35 -     4.90: 15427
  Nonbonded interactions: 37160
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 228 "
            pdb=" OD1 ASP A 229 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   GLU A 603 "
            pdb=" N   GLU A 606 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" OD2 ASP A 396 "
            pdb=" ND2 ASN A 398 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" OD1 ASP A 210 "
            pdb=" OE1 GLU A 211 "
     model   vdw
     2.463 3.040
  nonbonded pdb=" O   LYS A 168 "
            pdb=" N   LEU A 189 "
     model   vdw
     2.463 3.120
  ... (remaining 37155 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:                  0.010
  Normalize map: mean=0, sd=1:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.540
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
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      :  0.018   0.637   4751  Z= 1.046
  Angle     :  1.695  20.028   6473  Z= 1.193
  Chirality :  0.096   0.280    732
  Planarity :  0.010   0.099    830
  Dihedral  : 11.236  89.908   1687
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  2.45 %
    Favored  : 95.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.42 (0.32), residues: 591
  helix:  0.82 (0.45), residues: 102
  sheet:  1.14 (0.36), residues: 181
  loop : -0.41 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.007   TRP A 519 
 HIS   0.008   0.002   HIS A 616 
 PHE   0.027   0.003   PHE A 218 
 TYR   0.042   0.006   TYR A 257 
 ARG   0.006   0.001   ARG A 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17408 (  193)
  hydrogen bonds       : angle       8.22859 (  528)
  SS BOND              : bond        0.63715 (    1)
  SS BOND              : angle      14.27622 (    2)
  covalent geometry    : bond        0.01526 ( 4749)
  covalent geometry    : angle       1.67645 ( 6471)
  Misc. bond           : bond        0.09024 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 215
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 TRP cc_start: 0.8855 (m100) cc_final: 0.8528 (m100)
REVERT: A  278 TRP cc_start: 0.8463 (m100) cc_final: 0.7825 (m100)
REVERT: A  291 LEU cc_start: 0.8252 (tp) cc_final: 0.8009 (tt)
REVERT: A  347 THR cc_start: 0.8325 (p) cc_final: 0.8070 (p)
REVERT: A  357 ASP cc_start: 0.7081 (m-30) cc_final: 0.6704 (m-30)
REVERT: A  427 LEU cc_start: 0.7624 (tp) cc_final: 0.7387 (pt)
REVERT: A  429 GLU cc_start: 0.7842 (mp0) cc_final: 0.7501 (mp0)
REVERT: A  462 HIS cc_start: 0.8286 (p90) cc_final: 0.7905 (p90)
REVERT: A  601 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8487 (tt)
REVERT: A  621 LYS cc_start: 0.8190 (tttt) cc_final: 0.7846 (tppt)
  outliers start: 10
  outliers final: 1
  residues processed: 217
  average time/residue: 0.1653
  time to fit residues: 44.5596
Evaluate side-chains
  116 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
A 346 ASN
A 365 HIS
A 470 GLN
A 616 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.135871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.109176 restraints weight = 8571.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.113344 restraints weight = 4577.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.116214 restraints weight = 2949.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4751  Z= 0.154
  Angle     :  0.669   6.650   6473  Z= 0.361
  Chirality :  0.047   0.173    732
  Planarity :  0.004   0.029    830
  Dihedral  :  5.158  20.500    639
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  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:  0.43 (0.33), residues: 591
  helix:  1.11 (0.46), residues: 115
  sheet:  0.76 (0.37), residues: 180
  loop : -0.29 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 502 
 HIS   0.004   0.001   HIS A 228 
 PHE   0.012   0.002   PHE A 705 
 TYR   0.028   0.002   TYR A 169 
 ARG   0.006   0.001   ARG A 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05092 (  193)
  hydrogen bonds       : angle       6.11910 (  528)
  SS BOND              : bond        0.01527 (    1)
  SS BOND              : angle       1.13233 (    2)
  covalent geometry    : bond        0.00333 ( 4749)
  covalent geometry    : angle       0.66903 ( 6471)
  Misc. bond           : bond        0.00409 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ILE cc_start: 0.9149 (mm) cc_final: 0.8895 (mm)
REVERT: A  207 TRP cc_start: 0.8658 (m100) cc_final: 0.8195 (m100)
REVERT: A  223 ARG cc_start: 0.7956 (ptp-110) cc_final: 0.7594 (ptp-170)
REVERT: A  230 VAL cc_start: 0.9244 (t) cc_final: 0.8940 (p)
REVERT: A  261 ASP cc_start: 0.8799 (p0) cc_final: 0.8456 (p0)
REVERT: A  278 TRP cc_start: 0.8219 (m100) cc_final: 0.7855 (m100)
REVERT: A  346 ASN cc_start: 0.8554 (m-40) cc_final: 0.8225 (m-40)
REVERT: A  418 TYR cc_start: 0.6880 (m-80) cc_final: 0.6319 (m-80)
REVERT: A  427 LEU cc_start: 0.8408 (tp) cc_final: 0.7913 (pt)
REVERT: A  558 PHE cc_start: 0.8016 (t80) cc_final: 0.7707 (t80)
REVERT: A  601 LEU cc_start: 0.8964 (pp) cc_final: 0.8635 (tt)
REVERT: A  621 LYS cc_start: 0.8204 (tttt) cc_final: 0.7374 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1282
  time to fit residues: 26.4396
Evaluate side-chains
  102 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   chunk 16 optimal weight:    8.9990
   chunk 51 optimal weight:    0.0040
   chunk 30 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.9998

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

Flipped N/Q/H residues before XYZ refinement:
A 407 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.130721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.103379 restraints weight = 8691.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.107208 restraints weight = 4833.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.109873 restraints weight = 3231.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.4080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4751  Z= 0.188
  Angle     :  0.666   9.648   6473  Z= 0.357
  Chirality :  0.047   0.160    732
  Planarity :  0.004   0.034    830
  Dihedral  :  4.914  16.903    639
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  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:  0.36 (0.34), residues: 591
  helix:  1.34 (0.48), residues: 113
  sheet:  0.67 (0.40), residues: 163
  loop : -0.36 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 519 
 HIS   0.006   0.002   HIS A 228 
 PHE   0.014   0.002   PHE A 264 
 TYR   0.014   0.002   TYR A 623 
 ARG   0.002   0.000   ARG A 491 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04521 (  193)
  hydrogen bonds       : angle       5.57871 (  528)
  SS BOND              : bond        0.01151 (    1)
  SS BOND              : angle       1.85136 (    2)
  covalent geometry    : bond        0.00412 ( 4749)
  covalent geometry    : angle       0.66529 ( 6471)
  Misc. bond           : bond        0.00258 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LYS cc_start: 0.8404 (pttm) cc_final: 0.8157 (ttpp)
REVERT: A  207 TRP cc_start: 0.8716 (m100) cc_final: 0.8441 (m100)
REVERT: A  223 ARG cc_start: 0.7923 (ptp-110) cc_final: 0.7702 (ptp-110)
REVERT: A  261 ASP cc_start: 0.8810 (p0) cc_final: 0.8486 (p0)
REVERT: A  278 TRP cc_start: 0.8277 (m100) cc_final: 0.7737 (m100)
REVERT: A  327 THR cc_start: 0.7371 (t) cc_final: 0.6983 (t)
REVERT: A  346 ASN cc_start: 0.8386 (m-40) cc_final: 0.7987 (m-40)
REVERT: A  389 TRP cc_start: 0.9210 (p-90) cc_final: 0.8999 (p-90)
REVERT: A  427 LEU cc_start: 0.8519 (tp) cc_final: 0.8058 (pt)
REVERT: A  500 ASP cc_start: 0.8424 (t0) cc_final: 0.7849 (t0)
REVERT: A  554 THR cc_start: 0.9350 (m) cc_final: 0.9042 (p)
REVERT: A  601 LEU cc_start: 0.9078 (pp) cc_final: 0.8712 (tt)
REVERT: A  621 LYS cc_start: 0.8368 (tttt) cc_final: 0.7547 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1598
  time to fit residues: 27.8277
Evaluate side-chains
  102 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 0 optimal weight:   50.0000
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 228 HIS
A 336 ASN
** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 628 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.131351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.102845 restraints weight = 8904.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.106853 restraints weight = 4979.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.109585 restraints weight = 3345.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.4702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4751  Z= 0.187
  Angle     :  0.628   7.095   6473  Z= 0.336
  Chirality :  0.046   0.163    732
  Planarity :  0.004   0.038    830
  Dihedral  :  4.925  16.502    639
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  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:  0.37 (0.34), residues: 591
  helix:  1.48 (0.48), residues: 113
  sheet:  0.72 (0.39), residues: 170
  loop : -0.46 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 607 
 HIS   0.006   0.001   HIS A 228 
 PHE   0.011   0.002   PHE A 362 
 TYR   0.034   0.002   TYR A 623 
 ARG   0.002   0.000   ARG A 494 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04180 (  193)
  hydrogen bonds       : angle       5.38381 (  528)
  SS BOND              : bond        0.00891 (    1)
  SS BOND              : angle       1.64150 (    2)
  covalent geometry    : bond        0.00416 ( 4749)
  covalent geometry    : angle       0.62740 ( 6471)
  Misc. bond           : bond        0.00202 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 MET cc_start: 0.8553 (tmm) cc_final: 0.8274 (tmm)
REVERT: A  207 TRP cc_start: 0.8731 (m100) cc_final: 0.8478 (m100)
REVERT: A  245 TYR cc_start: 0.8395 (t80) cc_final: 0.8000 (t80)
REVERT: A  261 ASP cc_start: 0.8801 (p0) cc_final: 0.8538 (p0)
REVERT: A  278 TRP cc_start: 0.8242 (m100) cc_final: 0.7991 (m100)
REVERT: A  346 ASN cc_start: 0.8260 (m-40) cc_final: 0.7939 (m-40)
REVERT: A  427 LEU cc_start: 0.8573 (tp) cc_final: 0.8147 (pt)
REVERT: A  500 ASP cc_start: 0.8478 (t0) cc_final: 0.7901 (t0)
REVERT: A  554 THR cc_start: 0.9363 (m) cc_final: 0.9147 (t)
REVERT: A  601 LEU cc_start: 0.9102 (pp) cc_final: 0.8750 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1364
  time to fit residues: 23.7150
Evaluate side-chains
  98 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 0 optimal weight:   50.0000
   chunk 46 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 508 HIS
A 628 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.129010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.100700 restraints weight = 8983.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.104583 restraints weight = 4990.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.107275 restraints weight = 3353.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.5135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4751  Z= 0.204
  Angle     :  0.635   6.434   6473  Z= 0.340
  Chirality :  0.046   0.148    732
  Planarity :  0.004   0.040    830
  Dihedral  :  4.922  16.376    639
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.10 (0.34), residues: 591
  helix:  1.28 (0.48), residues: 113
  sheet:  0.54 (0.40), residues: 176
  loop : -0.67 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 519 
 HIS   0.008   0.002   HIS A 508 
 PHE   0.021   0.002   PHE A 705 
 TYR   0.016   0.002   TYR A 301 
 ARG   0.005   0.001   ARG A 442 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04226 (  193)
  hydrogen bonds       : angle       5.29971 (  528)
  SS BOND              : bond        0.00963 (    1)
  SS BOND              : angle       1.71515 (    2)
  covalent geometry    : bond        0.00457 ( 4749)
  covalent geometry    : angle       0.63469 ( 6471)
  Misc. bond           : bond        0.00211 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.9356 (mt) cc_final: 0.9083 (mp)
REVERT: A  167 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8190 (mt-10)
REVERT: A  207 TRP cc_start: 0.8756 (m100) cc_final: 0.7837 (m100)
REVERT: A  217 LEU cc_start: 0.9287 (tp) cc_final: 0.8762 (tp)
REVERT: A  223 ARG cc_start: 0.7892 (ptp-170) cc_final: 0.7581 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7672 (m-80) cc_final: 0.7216 (m-10)
REVERT: A  238 ASN cc_start: 0.7904 (m-40) cc_final: 0.7655 (m-40)
REVERT: A  245 TYR cc_start: 0.8312 (t80) cc_final: 0.7799 (t80)
REVERT: A  346 ASN cc_start: 0.8135 (m-40) cc_final: 0.7788 (m-40)
REVERT: A  370 TYR cc_start: 0.8148 (m-80) cc_final: 0.7876 (m-10)
REVERT: A  490 PHE cc_start: 0.9110 (t80) cc_final: 0.8903 (t80)
REVERT: A  500 ASP cc_start: 0.8545 (t0) cc_final: 0.8025 (t0)
REVERT: A  601 LEU cc_start: 0.9137 (pp) cc_final: 0.8810 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1324
  time to fit residues: 21.0750
Evaluate side-chains
  94 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0070
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.2004

-------------------------------------------------------------------------------
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 = 0.3700 r_free = 0.3700 target = 0.131217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.103113 restraints weight = 8776.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.107021 restraints weight = 4883.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.109706 restraints weight = 3270.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.5382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4751  Z= 0.135
  Angle     :  0.598   6.518   6473  Z= 0.318
  Chirality :  0.046   0.152    732
  Planarity :  0.004   0.036    830
  Dihedral  :  4.807  19.805    639
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.23 %
    Favored  : 98.57 %
  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:  0.16 (0.34), residues: 591
  helix:  1.57 (0.49), residues: 114
  sheet:  0.58 (0.40), residues: 171
  loop : -0.73 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 389 
 HIS   0.008   0.001   HIS A 228 
 PHE   0.021   0.002   PHE A 705 
 TYR   0.017   0.001   TYR A 301 
 ARG   0.002   0.000   ARG A 226 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03876 (  193)
  hydrogen bonds       : angle       5.26044 (  528)
  SS BOND              : bond        0.00739 (    1)
  SS BOND              : angle       1.45298 (    2)
  covalent geometry    : bond        0.00301 ( 4749)
  covalent geometry    : angle       0.59741 ( 6471)
  Misc. bond           : bond        0.00162 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.9344 (mt) cc_final: 0.9066 (mp)
REVERT: A  167 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8214 (mt-10)
REVERT: A  195 MET cc_start: 0.8481 (tmm) cc_final: 0.8218 (tmm)
REVERT: A  207 TRP cc_start: 0.8695 (m100) cc_final: 0.7734 (m100)
REVERT: A  217 LEU cc_start: 0.9224 (tp) cc_final: 0.8732 (tp)
REVERT: A  223 ARG cc_start: 0.7905 (ptp-170) cc_final: 0.7567 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7562 (m-80) cc_final: 0.7057 (m-10)
REVERT: A  238 ASN cc_start: 0.7946 (m-40) cc_final: 0.7683 (m-40)
REVERT: A  245 TYR cc_start: 0.8382 (t80) cc_final: 0.7730 (t80)
REVERT: A  346 ASN cc_start: 0.8085 (m-40) cc_final: 0.7780 (m-40)
REVERT: A  370 TYR cc_start: 0.8076 (m-80) cc_final: 0.7810 (m-10)
REVERT: A  427 LEU cc_start: 0.8497 (tp) cc_final: 0.7910 (pt)
REVERT: A  490 PHE cc_start: 0.9136 (t80) cc_final: 0.8859 (t80)
REVERT: A  500 ASP cc_start: 0.8601 (t0) cc_final: 0.8027 (t0)
REVERT: A  601 LEU cc_start: 0.9146 (pp) cc_final: 0.8836 (tt)
REVERT: A  624 CYS cc_start: 0.8938 (t) cc_final: 0.8642 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1393
  time to fit residues: 23.8565
Evaluate side-chains
  97 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 40 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 31 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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 = 0.3663 r_free = 0.3663 target = 0.128709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.099983 restraints weight = 8962.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.103756 restraints weight = 5074.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.106311 restraints weight = 3467.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.5718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4751  Z= 0.184
  Angle     :  0.626   6.686   6473  Z= 0.332
  Chirality :  0.046   0.151    732
  Planarity :  0.004   0.037    830
  Dihedral  :  4.893  23.029    639
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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:  0.05 (0.34), residues: 591
  helix:  1.65 (0.49), residues: 112
  sheet:  0.50 (0.39), residues: 176
  loop : -0.88 (0.33), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 389 
 HIS   0.006   0.001   HIS A 228 
 PHE   0.015   0.002   PHE A 255 
 TYR   0.013   0.001   TYR A 301 
 ARG   0.002   0.000   ARG A 577 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  193)
  hydrogen bonds       : angle       5.34343 (  528)
  SS BOND              : bond        0.00938 (    1)
  SS BOND              : angle       1.52134 (    2)
  covalent geometry    : bond        0.00407 ( 4749)
  covalent geometry    : angle       0.62509 ( 6471)
  Misc. bond           : bond        0.00186 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7719 (t) cc_final: 0.7466 (p)
REVERT: A  145 LEU cc_start: 0.9369 (mt) cc_final: 0.9124 (mp)
REVERT: A  207 TRP cc_start: 0.8822 (m100) cc_final: 0.7944 (m100)
REVERT: A  217 LEU cc_start: 0.9271 (tp) cc_final: 0.8755 (tp)
REVERT: A  223 ARG cc_start: 0.7781 (ptp-170) cc_final: 0.7476 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7689 (m-80) cc_final: 0.7231 (m-10)
REVERT: A  245 TYR cc_start: 0.8335 (t80) cc_final: 0.7689 (t80)
REVERT: A  346 ASN cc_start: 0.8000 (m-40) cc_final: 0.7697 (m-40)
REVERT: A  427 LEU cc_start: 0.8495 (tp) cc_final: 0.7967 (pt)
REVERT: A  495 ARG cc_start: 0.8521 (ttt-90) cc_final: 0.8235 (tpt-90)
REVERT: A  500 ASP cc_start: 0.8597 (t0) cc_final: 0.8161 (t0)
REVERT: A  514 GLU cc_start: 0.7637 (pm20) cc_final: 0.7406 (pm20)
REVERT: A  558 PHE cc_start: 0.8476 (t80) cc_final: 0.7941 (t80)
REVERT: A  559 SER cc_start: 0.9470 (p) cc_final: 0.9269 (p)
REVERT: A  601 LEU cc_start: 0.9185 (pp) cc_final: 0.8884 (tt)
REVERT: A  624 CYS cc_start: 0.8932 (t) cc_final: 0.8652 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1348
  time to fit residues: 21.6208
Evaluate side-chains
  91 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 48 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
** A 228 HIS ** 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 = 0.3643 r_free = 0.3643 target = 0.127073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.098294 restraints weight = 9029.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.102002 restraints weight = 5106.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.104528 restraints weight = 3497.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.5921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4751  Z= 0.239
  Angle     :  0.668   6.736   6473  Z= 0.354
  Chirality :  0.047   0.154    732
  Planarity :  0.004   0.037    830
  Dihedral  :  5.044  21.248    639
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  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: -0.17 (0.34), residues: 591
  helix:  1.75 (0.49), residues: 111
  sheet:  0.27 (0.39), residues: 172
  loop : -1.05 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 389 
 HIS   0.024   0.002   HIS A 228 
 PHE   0.013   0.002   PHE A 490 
 TYR   0.015   0.002   TYR A 169 
 ARG   0.004   0.000   ARG A 226 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04300 (  193)
  hydrogen bonds       : angle       5.50460 (  528)
  SS BOND              : bond        0.01011 (    1)
  SS BOND              : angle       1.95653 (    2)
  covalent geometry    : bond        0.00527 ( 4749)
  covalent geometry    : angle       0.66719 ( 6471)
  Misc. bond           : bond        0.00187 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7840 (t) cc_final: 0.7503 (p)
REVERT: A  145 LEU cc_start: 0.9392 (mt) cc_final: 0.9164 (mp)
REVERT: A  195 MET cc_start: 0.8555 (tmm) cc_final: 0.8332 (tmm)
REVERT: A  207 TRP cc_start: 0.8813 (m100) cc_final: 0.8051 (m100)
REVERT: A  217 LEU cc_start: 0.9305 (tp) cc_final: 0.8988 (tp)
REVERT: A  231 TYR cc_start: 0.7747 (m-80) cc_final: 0.7474 (m-10)
REVERT: A  245 TYR cc_start: 0.8276 (t80) cc_final: 0.7658 (t80)
REVERT: A  346 ASN cc_start: 0.8036 (m-40) cc_final: 0.7831 (m-40)
REVERT: A  462 HIS cc_start: 0.8894 (p90) cc_final: 0.8636 (p90)
REVERT: A  500 ASP cc_start: 0.8685 (t0) cc_final: 0.8350 (t0)
REVERT: A  601 LEU cc_start: 0.9216 (pp) cc_final: 0.8907 (tt)
REVERT: A  621 LYS cc_start: 0.8668 (tttt) cc_final: 0.7980 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1460
  time to fit residues: 20.5646
Evaluate side-chains
  85 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0870
   chunk 18 optimal weight:    0.4980
   chunk 51 optimal weight:    0.2980
   chunk 4 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.7762

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 HIS ** 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 = 0.3704 r_free = 0.3704 target = 0.131526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.103279 restraints weight = 8833.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.107086 restraints weight = 4867.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.109672 restraints weight = 3279.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.5994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4751  Z= 0.116
  Angle     :  0.583   6.838   6473  Z= 0.309
  Chirality :  0.045   0.155    732
  Planarity :  0.004   0.036    830
  Dihedral  :  4.736  22.563    639
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  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:  0.02 (0.34), residues: 591
  helix:  1.76 (0.50), residues: 114
  sheet:  0.32 (0.40), residues: 174
  loop : -0.85 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 389 
 HIS   0.008   0.001   HIS A 228 
 PHE   0.014   0.001   PHE A 393 
 TYR   0.016   0.001   TYR A 623 
 ARG   0.003   0.000   ARG A 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03707 (  193)
  hydrogen bonds       : angle       5.24763 (  528)
  SS BOND              : bond        0.00758 (    1)
  SS BOND              : angle       1.22680 (    2)
  covalent geometry    : bond        0.00256 ( 4749)
  covalent geometry    : angle       0.58309 ( 6471)
  Misc. bond           : bond        0.00149 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7828 (t) cc_final: 0.7546 (p)
REVERT: A  145 LEU cc_start: 0.9374 (mt) cc_final: 0.9142 (mp)
REVERT: A  167 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8193 (mt-10)
REVERT: A  195 MET cc_start: 0.8571 (tmm) cc_final: 0.8348 (tmm)
REVERT: A  207 TRP cc_start: 0.8757 (m100) cc_final: 0.7817 (m100)
REVERT: A  217 LEU cc_start: 0.9201 (tp) cc_final: 0.8738 (tp)
REVERT: A  231 TYR cc_start: 0.7763 (m-80) cc_final: 0.7484 (m-10)
REVERT: A  245 TYR cc_start: 0.8392 (t80) cc_final: 0.7766 (t80)
REVERT: A  346 ASN cc_start: 0.7769 (m-40) cc_final: 0.7499 (m-40)
REVERT: A  347 THR cc_start: 0.8994 (m) cc_final: 0.8678 (p)
REVERT: A  427 LEU cc_start: 0.8477 (tp) cc_final: 0.7981 (pt)
REVERT: A  488 MET cc_start: 0.8726 (mmm) cc_final: 0.7840 (mmm)
REVERT: A  601 LEU cc_start: 0.9191 (pp) cc_final: 0.8897 (tt)
REVERT: A  621 LYS cc_start: 0.8523 (tttt) cc_final: 0.7868 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1435
  time to fit residues: 23.2914
Evaluate side-chains
  92 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 30 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0270
   chunk 29 optimal weight:    0.2980
   chunk 15 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.6040

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 HIS ** 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 = 0.3706 r_free = 0.3706 target = 0.131813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.102601 restraints weight = 8933.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.106472 restraints weight = 5029.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.109086 restraints weight = 3421.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.6151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4751  Z= 0.114
  Angle     :  0.585   6.666   6473  Z= 0.307
  Chirality :  0.045   0.154    732
  Planarity :  0.004   0.036    830
  Dihedral  :  4.575  21.673    639
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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:  0.12 (0.34), residues: 591
  helix:  1.81 (0.51), residues: 113
  sheet:  0.31 (0.38), residues: 184
  loop : -0.74 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 389 
 HIS   0.008   0.001   HIS A 228 
 PHE   0.012   0.001   PHE A 393 
 TYR   0.016   0.001   TYR A 623 
 ARG   0.002   0.000   ARG A 226 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03658 (  193)
  hydrogen bonds       : angle       5.15557 (  528)
  SS BOND              : bond        0.00731 (    1)
  SS BOND              : angle       1.40246 (    2)
  covalent geometry    : bond        0.00257 ( 4749)
  covalent geometry    : angle       0.58413 ( 6471)
  Misc. bond           : bond        0.00203 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7798 (t) cc_final: 0.7485 (p)
REVERT: A  145 LEU cc_start: 0.9374 (mt) cc_final: 0.9157 (mp)
REVERT: A  167 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8177 (mt-10)
REVERT: A  195 MET cc_start: 0.8572 (tmm) cc_final: 0.8324 (tmm)
REVERT: A  207 TRP cc_start: 0.8729 (m100) cc_final: 0.7802 (m100)
REVERT: A  217 LEU cc_start: 0.9181 (tp) cc_final: 0.8722 (tp)
REVERT: A  231 TYR cc_start: 0.7765 (m-80) cc_final: 0.7496 (m-10)
REVERT: A  245 TYR cc_start: 0.8385 (t80) cc_final: 0.7758 (t80)
REVERT: A  327 THR cc_start: 0.7405 (m) cc_final: 0.6967 (m)
REVERT: A  346 ASN cc_start: 0.7643 (m-40) cc_final: 0.7425 (m-40)
REVERT: A  347 THR cc_start: 0.8879 (m) cc_final: 0.8591 (p)
REVERT: A  427 LEU cc_start: 0.8517 (tp) cc_final: 0.8025 (pt)
REVERT: A  488 MET cc_start: 0.8687 (mmm) cc_final: 0.7907 (mmm)
REVERT: A  500 ASP cc_start: 0.8898 (t70) cc_final: 0.8577 (t0)
REVERT: A  601 LEU cc_start: 0.9182 (pp) cc_final: 0.8909 (tt)
REVERT: A  621 LYS cc_start: 0.8531 (tttt) cc_final: 0.7832 (tppt)
REVERT: A  628 ASN cc_start: 0.9131 (m-40) cc_final: 0.8895 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1360
  time to fit residues: 22.0299
Evaluate side-chains
  95 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 32 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 53 optimal weight:    0.0070
   chunk 8 optimal weight:    6.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 644 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.133121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.103727 restraints weight = 8937.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.107708 restraints weight = 5029.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.110372 restraints weight = 3408.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.6188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4751  Z= 0.113
  Angle     :  0.576   8.124   6473  Z= 0.301
  Chirality :  0.045   0.157    732
  Planarity :  0.004   0.035    830
  Dihedral  :  4.480  20.824    639
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.00 %
    Favored  : 99.80 %
  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:  0.19 (0.34), residues: 591
  helix:  1.87 (0.51), residues: 114
  sheet:  0.29 (0.38), residues: 184
  loop : -0.66 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 389 
 HIS   0.008   0.001   HIS A 462 
 PHE   0.013   0.001   PHE A 393 
 TYR   0.016   0.001   TYR A 623 
 ARG   0.002   0.000   ARG A 226 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03519 (  193)
  hydrogen bonds       : angle       5.08714 (  528)
  SS BOND              : bond        0.00730 (    1)
  SS BOND              : angle       1.56427 (    2)
  covalent geometry    : bond        0.00254 ( 4749)
  covalent geometry    : angle       0.57499 ( 6471)
  Misc. bond           : bond        0.00044 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1755.80 seconds
wall clock time: 31 minutes 21.71 seconds (1881.71 seconds total)