Starting phenix.real_space_refine
on Sat May 10 02:25:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hb0_34610/05_2025/8hb0_34610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hb0_34610/05_2025/8hb0_34610.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hb0_34610/05_2025/8hb0_34610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hb0_34610/05_2025/8hb0_34610.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hb0_34610/05_2025/8hb0_34610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hb0_34610/05_2025/8hb0_34610.cif"
  }
  resolution = 2.9
  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=   0.001 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     Na      1      4.78       5
     C    3153      2.51       5
     N     777      2.21       5
     O     809      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 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: 4778
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 586, 4497
          Classifications: {'peptide': 586}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 558}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 231
          Classifications: {'peptide': 29}
          Link IDs: {'PTRANS': 1, 'TRANS': 27}
    Chain: "A"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 50
          Unusual residues: {' NA': 1, 'KZ3': 1, 'NAG': 1}
          Classifications: {'undetermined': 3, 'water': 4}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.32, per 1000 atoms: 0.69
  Number of scatterers: 4778
  At special positions: 0
  Unit cell: (73.0402, 75.2536, 92.9603, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      37     16.00
     Na      1     11.00
     F       1      9.00
     O     809      8.00
     N     777      7.00
     C    3153      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 255 " - pdb=" SG  CYS A 511 " distance=2.20
    Simple disulfide: pdb=" SG  CYS A 345 " - pdb=" SG  CYS A 351 " distance=2.32
    Simple disulfide: pdb=" SG  CYS A 355 " - pdb=" SG  CYS A 361 " distance=2.33
    Simple disulfide: pdb=" SG  CYS A 517 " - pdb=" SG  CYS A 522 " distance=2.35

  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: 1.11
  Conformation dependent library (CDL) restraints added in 552.6 milliseconds
  

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1116

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      82.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 47
      removed outlier: 3.997A  pdb=" N   ILE A  26 " --> pdb=" O   ASN A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 58
    Processing helix  chain 'A' and resid 59 through 61
      No H-bonds generated for 'chain 'A' and resid 59 through 61'
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 77 through 92
      removed outlier: 3.760A  pdb=" N   PHE A  81 " --> pdb=" O   GLY A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 112
      removed outlier: 4.115A  pdb=" N   GLU A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA A 102 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU A 103 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   PHE A 104 " --> pdb=" O   TRP A 100 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU A 108 " --> pdb=" O   PHE A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 121
      removed outlier: 4.095A  pdb=" N   VAL A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 134
    Processing helix  chain 'A' and resid 136 through 154
      removed outlier: 3.643A  pdb=" N   LEU A 140 " --> pdb=" O   ARG A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 170
      removed outlier: 3.569A  pdb=" N   ASP A 158 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 192
      removed outlier: 4.180A  pdb=" N   GLY A 192 " --> pdb=" O   TYR A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 224
      removed outlier: 3.736A  pdb=" N   LEU A 197 " --> pdb=" O   GLY A 193 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 233
      removed outlier: 3.504A  pdb=" N   LEU A 229 " --> pdb=" O   GLY A 225 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE A 230 " --> pdb=" O   TYR A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 257
      removed outlier: 3.721A  pdb=" N   TYR A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ARG A 257 " --> pdb=" O   SER A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 252 through 257'
    Processing helix  chain 'A' and resid 275 through 293
    Processing helix  chain 'A' and resid 294 through 299
    Processing helix  chain 'A' and resid 306 through 323
      removed outlier: 3.758A  pdb=" N   THR A 323 " --> pdb=" O   TYR A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 328
    Processing helix  chain 'A' and resid 328 through 339
    Processing helix  chain 'A' and resid 339 through 344
    Processing helix  chain 'A' and resid 347 through 355
    Processing helix  chain 'A' and resid 361 through 363
      No H-bonds generated for 'chain 'A' and resid 361 through 363'
    Processing helix  chain 'A' and resid 364 through 374
      removed outlier: 3.560A  pdb=" N   LEU A 369 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL A 371 " --> pdb=" O   PRO A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 409
      removed outlier: 4.025A  pdb=" N   LEU A 381 " --> pdb=" O   GLY A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 414
    Processing helix  chain 'A' and resid 420 through 446
      removed outlier: 3.539A  pdb=" N   VAL A 430 " --> pdb=" O   GLY A 426 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL A 431 " --> pdb=" O   ARG A 427 " (cutoff:3.500A)
      Proline residue:  A 442  - end of helix
    Processing helix  chain 'A' and resid 450 through 464
      removed outlier: 3.646A  pdb=" N   ASP A 454 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 477
    Processing helix  chain 'A' and resid 481 through 507
      Proline residue:  A 502  - end of helix
    Processing helix  chain 'A' and resid 518 through 524
      removed outlier: 4.243A  pdb=" N   VAL A 524 " --> pdb=" O   PHE A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 548
      removed outlier: 3.625A  pdb=" N   ILE A 531 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 556
    Processing helix  chain 'A' and resid 646 through 671
    Processing helix  chain 'B' and resid 29 through 55

    342 hydrogen bonds defined for protein.
    1020 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: 1.32

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 701
        1.28 -     1.42: 1349
        1.42 -     1.56: 2797
        1.56 -     1.70: 0
        1.70 -     1.84: 57
  Bond restraints: 4904
  Sorted by residual:
  bond pdb=" C   PRO A 324 "
       pdb=" O   PRO A 324 "
    ideal  model  delta    sigma   weight residual
    1.237  1.139  0.099 1.26e-02 6.30e+03 6.14e+01
  bond pdb=" C   PRO A 502 "
       pdb=" O   PRO A 502 "
    ideal  model  delta    sigma   weight residual
    1.235  1.145  0.090 1.30e-02 5.92e+03 4.78e+01
  bond pdb=" C   LEU A 497 "
       pdb=" O   LEU A 497 "
    ideal  model  delta    sigma   weight residual
    1.237  1.170  0.066 1.19e-02 7.06e+03 3.10e+01
  bond pdb=" C   PRO A  66 "
       pdb=" O   PRO A  66 "
    ideal  model  delta    sigma   weight residual
    1.237  1.170  0.067 1.29e-02 6.01e+03 2.68e+01
  bond pdb=" C   PHE A 520 "
       pdb=" O   PHE A 520 "
    ideal  model  delta    sigma   weight residual
    1.235  1.299 -0.063 1.26e-02 6.30e+03 2.53e+01
  ... (remaining 4899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 4600
        2.24 -     4.48: 1803
        4.48 -     6.72: 264
        6.72 -     8.96: 17
        8.96 -    11.20: 8
  Bond angle restraints: 6692
  Sorted by residual:
  angle pdb=" CA  ASP A 261 "
        pdb=" CB  ASP A 261 "
        pdb=" CG  ASP A 261 "
      ideal   model   delta    sigma   weight residual
     112.60  119.21   -6.61 1.00e+00 1.00e+00 4.37e+01
  angle pdb=" CA  PHE A 326 "
        pdb=" CB  PHE A 326 "
        pdb=" CG  PHE A 326 "
      ideal   model   delta    sigma   weight residual
     113.80  107.31    6.49 1.00e+00 1.00e+00 4.22e+01
  angle pdb=" CA  PHE A 520 "
        pdb=" CB  PHE A 520 "
        pdb=" CG  PHE A 520 "
      ideal   model   delta    sigma   weight residual
     113.80  120.25   -6.45 1.00e+00 1.00e+00 4.16e+01
  angle pdb=" C   SER A 227 "
        pdb=" N   GLY A 228 "
        pdb=" CA  GLY A 228 "
      ideal   model   delta    sigma   weight residual
     120.03  127.10   -7.07 1.12e+00 7.97e-01 3.98e+01
  angle pdb=" C   ARG A 420 "
        pdb=" N   GLU A 421 "
        pdb=" CA  GLU A 421 "
      ideal   model   delta    sigma   weight residual
     120.44  128.50   -8.06 1.30e+00 5.92e-01 3.85e+01
  ... (remaining 6687 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.08: 2572
       16.08 -    32.16: 219
       32.16 -    48.24: 45
       48.24 -    64.33: 14
       64.33 -    80.41: 4
  Dihedral angle restraints: 2854
    sinusoidal: 1102
      harmonic: 1752
  Sorted by residual:
  dihedral pdb=" CB  CYS A 517 "
           pdb=" SG  CYS A 517 "
           pdb=" SG  CYS A 522 "
           pdb=" CB  CYS A 522 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   12.59   80.41     1      1.00e+01 1.00e-02 8.00e+01
  dihedral pdb=" CA  GLY A 418 "
           pdb=" C   GLY A 418 "
           pdb=" N   ASP A 419 "
           pdb=" CA  ASP A 419 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.03  -25.97     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" C   GLU A 503 "
           pdb=" N   GLU A 503 "
           pdb=" CA  GLU A 503 "
           pdb=" CB  GLU A 503 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.19  -12.41     0      2.50e+00 1.60e-01 2.46e+01
  ... (remaining 2851 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 387
       0.059 -    0.118: 232
       0.118 -    0.177: 116
       0.177 -    0.236: 39
       0.236 -    0.295: 5
  Chirality restraints: 779
  Sorted by residual:
  chirality pdb=" CA  PRO A 269 "
            pdb=" N   PRO A 269 "
            pdb=" C   PRO A 269 "
            pdb=" CB  PRO A 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.42    0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CB  VAL A 106 "
            pdb=" CA  VAL A 106 "
            pdb=" CG1 VAL A 106 "
            pdb=" CG2 VAL A 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.15e+00
  chirality pdb=" CA  VAL A 560 "
            pdb=" N   VAL A 560 "
            pdb=" C   VAL A 560 "
            pdb=" CB  VAL A 560 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.56e+00
  ... (remaining 776 not shown)

  Planarity restraints: 817
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 801 "   -0.043 2.00e-02 2.50e+03   3.51e-02 1.54e+01
        pdb=" C7  NAG A 801 "    0.012 2.00e-02 2.50e+03
        pdb=" C8  NAG A 801 "   -0.033 2.00e-02 2.50e+03
        pdb=" N2  NAG A 801 "    0.055 2.00e-02 2.50e+03
        pdb=" O7  NAG A 801 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 521 "    0.016 2.00e-02 2.50e+03   3.08e-02 9.46e+00
        pdb=" C   LEU A 521 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   LEU A 521 "    0.019 2.00e-02 2.50e+03
        pdb=" N   CYS A 522 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 520 "   -0.014 2.00e-02 2.50e+03   2.87e-02 8.25e+00
        pdb=" C   PHE A 520 "    0.050 2.00e-02 2.50e+03
        pdb=" O   PHE A 520 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LEU A 521 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 814 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 104
        2.70 -     3.25: 4833
        3.25 -     3.80: 7942
        3.80 -     4.35: 10878
        4.35 -     4.90: 17609
  Nonbonded interactions: 41366
  Sorted by model distance:
  nonbonded pdb=" O   ALA A  73 "
            pdb="NA    NA A 803 "
     model   vdw
     2.153 2.470
  nonbonded pdb=" O   ILE A  76 "
            pdb="NA    NA A 803 "
     model   vdw
     2.267 2.470
  nonbonded pdb=" OG  SER A 392 "
            pdb="NA    NA A 803 "
     model   vdw
     2.299 2.470
  nonbonded pdb=" O   GLY A 332 "
            pdb=" OG  SER A 335 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" ND2 ASN A 250 "
            pdb=" C1  NAG A 801 "
     model   vdw
     2.344 3.550
  ... (remaining 41361 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:             0.110
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.770
  Find NCS groups from input model:        0.040
  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:11.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
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      :  0.017   0.318   4908  Z= 1.207
  Angle     :  2.311  40.549   6700  Z= 1.681
  Chirality :  0.091   0.295    779
  Planarity :  0.005   0.035    817
  Dihedral  : 13.362  80.313   1726
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.94 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  5.80 %
    Favored  : 93.40 %
  Cbeta Deviations :  0.72 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.30 (0.30), residues: 609
  helix: -1.34 (0.20), residues: 444
  sheet:  None (None), residues: 0
  loop : -1.52 (0.50), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A 291 
 HIS   0.013   0.002   HIS A  80 
 PHE   0.023   0.004   PHE A 326 
 TYR   0.021   0.005   TYR A 128 
 ARG   0.006   0.001   ARG A 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19018 (  342)
  hydrogen bonds       : angle       8.71411 ( 1020)
  SS BOND              : bond        0.27721 (    4)
  SS BOND              : angle      19.03329 (    8)
  covalent geometry    : bond        0.01547 ( 4904)
  covalent geometry    : angle       2.21624 ( 6692)

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

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

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A   45 CYS cc_start: 0.8008 (m) cc_final: 0.7036 (p)
REVERT: A   49 ARG cc_start: 0.7408 (mtp-110) cc_final: 0.7151 (mtm180)
REVERT: A  148 PHE cc_start: 0.8062 (m-10) cc_final: 0.7841 (m-80)
REVERT: A  150 TYR cc_start: 0.8407 (m-10) cc_final: 0.8106 (m-10)
REVERT: A  167 GLN cc_start: 0.8132 (tt0) cc_final: 0.7689 (tm-30)
REVERT: A  254 PHE cc_start: 0.7582 (t80) cc_final: 0.7347 (t80)
REVERT: A  274 LEU cc_start: 0.8571 (mt) cc_final: 0.8362 (mt)
REVERT: A  325 MET cc_start: 0.8894 (tpp) cc_final: 0.8633 (tpp)
REVERT: A  353 ARG cc_start: 0.7686 (ttp-110) cc_final: 0.7140 (ttm110)
REVERT: A  407 MET cc_start: 0.8652 (mmm) cc_final: 0.8382 (mmm)
REVERT: A  420 ARG cc_start: 0.7444 (ttt180) cc_final: 0.6617 (ttp-110)
REVERT: A  548 THR cc_start: 0.7959 (m) cc_final: 0.7389 (p)
REVERT: A  560 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8097 (m)
REVERT: A  568 GLU cc_start: 0.6580 (mt-10) cc_final: 0.6109 (mt-10)
REVERT: A  641 GLU cc_start: 0.5285 (mm-30) cc_final: 0.4478 (pm20)
REVERT: A  661 MET cc_start: 0.7934 (mtt) cc_final: 0.7720 (mtm)
  outliers start: 4
  outliers final: 1
  residues processed: 96
  average time/residue: 1.0254
  time to fit residues: 102.8687
Evaluate side-chains
  57 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  502 PRO
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
A 295 GLN
A 483 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.119196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.098116 restraints weight = 5149.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 1.31
r_work: 0.2873 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4908  Z= 0.157
  Angle     :  0.685  12.615   6700  Z= 0.350
  Chirality :  0.043   0.143    779
  Planarity :  0.005   0.039    817
  Dihedral  :  4.833  18.144    726
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  :  8.00 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.76 (0.33), residues: 609
  helix:  1.05 (0.23), residues: 451
  sheet:  None (None), residues: 0
  loop : -0.94 (0.52), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  65 
 HIS   0.004   0.001   HIS A  80 
 PHE   0.015   0.002   PHE A 520 
 TYR   0.021   0.002   TYR A 256 
 ARG   0.004   0.001   ARG A 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04760 (  342)
  hydrogen bonds       : angle       5.77228 ( 1020)
  SS BOND              : bond        0.00649 (    4)
  SS BOND              : angle       1.64213 (    8)
  covalent geometry    : bond        0.00344 ( 4904)
  covalent geometry    : angle       0.68263 ( 6692)

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

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

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A   45 CYS cc_start: 0.7935 (m) cc_final: 0.7117 (p)
REVERT: A  231 ASP cc_start: 0.8390 (p0) cc_final: 0.8129 (p0)
REVERT: A  254 PHE cc_start: 0.7698 (t80) cc_final: 0.7429 (t80)
REVERT: A  281 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7230 (tt)
REVERT: A  300 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7359 (mmt180)
REVERT: A  407 MET cc_start: 0.8883 (mmm) cc_final: 0.8673 (mmt)
REVERT: A  416 ARG cc_start: 0.7301 (mpt180) cc_final: 0.7010 (mtm180)
REVERT: A  420 ARG cc_start: 0.7038 (ttt180) cc_final: 0.6709 (ttm-80)
REVERT: A  448 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8267 (mm-40)
REVERT: A  451 GLN cc_start: 0.8155 (mt0) cc_final: 0.7672 (mt0)
REVERT: A  515 SER cc_start: 0.7162 (p) cc_final: 0.6765 (m)
REVERT: A  548 THR cc_start: 0.7609 (m) cc_final: 0.7329 (p)
REVERT: A  661 MET cc_start: 0.8043 (mtt) cc_final: 0.7821 (mtm)
  outliers start: 12
  outliers final: 1
  residues processed: 82
  average time/residue: 1.1404
  time to fit residues: 97.4435
Evaluate side-chains
  65 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  448 GLN
Chi-restraints excluded: chain A residue  494 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3286 r_free = 0.3286 target = 0.121811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.099187 restraints weight = 4973.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.39
r_work: 0.2894 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4908  Z= 0.128
  Angle     :  0.616  13.052   6700  Z= 0.308
  Chirality :  0.041   0.146    779
  Planarity :  0.005   0.044    817
  Dihedral  :  4.299  17.678    722
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 10.00 %
    Favored  : 87.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.35), residues: 609
  helix:  1.73 (0.24), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.78 (0.53), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  65 
 HIS   0.003   0.001   HIS A  80 
 PHE   0.011   0.001   PHE A 520 
 TYR   0.013   0.002   TYR A 256 
 ARG   0.008   0.001   ARG A 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04160 (  342)
  hydrogen bonds       : angle       5.39116 ( 1020)
  SS BOND              : bond        0.00302 (    4)
  SS BOND              : angle       1.19099 (    8)
  covalent geometry    : bond        0.00272 ( 4904)
  covalent geometry    : angle       0.61515 ( 6692)

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

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

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.521 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7581 (mtp) cc_final: 0.7277 (mtm)
REVERT: A   45 CYS cc_start: 0.7918 (m) cc_final: 0.6974 (p)
REVERT: A   46 ARG cc_start: 0.6226 (ttt90) cc_final: 0.5885 (ttt-90)
REVERT: A  231 ASP cc_start: 0.8286 (p0) cc_final: 0.8055 (p0)
REVERT: A  254 PHE cc_start: 0.7633 (t80) cc_final: 0.7359 (t80)
REVERT: A  281 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6953 (tt)
REVERT: A  300 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7523 (mmt180)
REVERT: A  407 MET cc_start: 0.8775 (mmm) cc_final: 0.8563 (mmt)
REVERT: A  416 ARG cc_start: 0.7193 (mpt180) cc_final: 0.6905 (mtm180)
REVERT: A  420 ARG cc_start: 0.6918 (ttt180) cc_final: 0.6619 (ttm-80)
REVERT: A  448 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8307 (mm-40)
REVERT: A  451 GLN cc_start: 0.8105 (mt0) cc_final: 0.7586 (mt0)
REVERT: A  548 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7150 (p)
REVERT: A  661 MET cc_start: 0.7973 (mtt) cc_final: 0.7725 (mtm)
  outliers start: 13
  outliers final: 3
  residues processed: 69
  average time/residue: 1.2459
  time to fit residues: 89.3884
Evaluate side-chains
  66 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  412 ARG
Chi-restraints excluded: chain A residue  448 GLN
Chi-restraints excluded: chain A residue  548 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0570
   chunk 57 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0570
   chunk 44 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.5620

-------------------------------------------------------------------------------
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 = 0.3324 r_free = 0.3324 target = 0.124786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.102637 restraints weight = 5026.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 1.40
r_work: 0.2941 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2820 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4908  Z= 0.111
  Angle     :  0.576  12.778   6700  Z= 0.284
  Chirality :  0.039   0.140    779
  Planarity :  0.005   0.044    817
  Dihedral  :  4.017  17.998    722
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  :  9.80 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.35), residues: 609
  helix:  2.02 (0.24), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.67 (0.53), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  65 
 HIS   0.002   0.001   HIS A 555 
 PHE   0.009   0.001   PHE A 520 
 TYR   0.010   0.001   TYR A 290 
 ARG   0.007   0.000   ARG A 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  342)
  hydrogen bonds       : angle       5.11875 ( 1020)
  SS BOND              : bond        0.00200 (    4)
  SS BOND              : angle       0.86522 (    8)
  covalent geometry    : bond        0.00227 ( 4904)
  covalent geometry    : angle       0.57574 ( 6692)

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

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

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.512 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7473 (mtp) cc_final: 0.7208 (mtm)
REVERT: A   45 CYS cc_start: 0.7853 (m) cc_final: 0.6929 (p)
REVERT: A   46 ARG cc_start: 0.6190 (ttt90) cc_final: 0.5856 (ttt-90)
REVERT: A  254 PHE cc_start: 0.7563 (t80) cc_final: 0.7340 (t80)
REVERT: A  300 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7552 (mmt180)
REVERT: A  407 MET cc_start: 0.8757 (mmm) cc_final: 0.8535 (mmt)
REVERT: A  416 ARG cc_start: 0.7223 (mpt180) cc_final: 0.6885 (mtm180)
REVERT: A  420 ARG cc_start: 0.6820 (ttt180) cc_final: 0.6501 (ttm-80)
REVERT: A  448 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8279 (mm-40)
REVERT: A  451 GLN cc_start: 0.8083 (mt0) cc_final: 0.7597 (mt0)
REVERT: A  548 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7147 (p)
REVERT: A  661 MET cc_start: 0.7983 (mtt) cc_final: 0.7713 (mtm)
  outliers start: 16
  outliers final: 4
  residues processed: 78
  average time/residue: 1.1627
  time to fit residues: 94.6473
Evaluate side-chains
  68 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  412 ARG
Chi-restraints excluded: chain A residue  448 GLN
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  548 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 16 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 48 optimal weight:    6.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3296 r_free = 0.3296 target = 0.122218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.100806 restraints weight = 5107.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 1.30
r_work: 0.2914 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4908  Z= 0.124
  Angle     :  0.592  14.741   6700  Z= 0.291
  Chirality :  0.040   0.145    779
  Planarity :  0.005   0.045    817
  Dihedral  :  3.956  17.201    722
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 11.40 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.35), residues: 609
  helix:  2.04 (0.24), residues: 452
  sheet:  None (None), residues: 0
  loop : -0.53 (0.54), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 487 
 HIS   0.003   0.001   HIS A  80 
 PHE   0.009   0.001   PHE A 520 
 TYR   0.010   0.001   TYR A 128 
 ARG   0.004   0.000   ARG A 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03952 (  342)
  hydrogen bonds       : angle       5.23053 ( 1020)
  SS BOND              : bond        0.00227 (    4)
  SS BOND              : angle       0.75803 (    8)
  covalent geometry    : bond        0.00268 ( 4904)
  covalent geometry    : angle       0.59192 ( 6692)

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

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

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7562 (mtp) cc_final: 0.7236 (mtm)
REVERT: A   45 CYS cc_start: 0.7915 (m) cc_final: 0.6983 (p)
REVERT: A   46 ARG cc_start: 0.6101 (ttt90) cc_final: 0.5751 (ttt-90)
REVERT: A  281 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6704 (tt)
REVERT: A  300 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7519 (mmt180)
REVERT: A  349 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7424 (mp0)
REVERT: A  407 MET cc_start: 0.8753 (mmm) cc_final: 0.8529 (mmt)
REVERT: A  416 ARG cc_start: 0.7171 (mpt180) cc_final: 0.6918 (mtm180)
REVERT: A  451 GLN cc_start: 0.8192 (mt0) cc_final: 0.7776 (mt0)
REVERT: A  475 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8262 (tp)
REVERT: A  548 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7172 (p)
REVERT: A  568 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6078 (mt-10)
REVERT: A  661 MET cc_start: 0.7929 (mtt) cc_final: 0.7710 (mtm)
  outliers start: 17
  outliers final: 5
  residues processed: 72
  average time/residue: 1.3105
  time to fit residues: 97.8706
Evaluate side-chains
  69 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  548 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 557 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.120321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.099230 restraints weight = 5107.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.33
r_work: 0.2891 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2773 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4908  Z= 0.135
  Angle     :  0.604  15.312   6700  Z= 0.298
  Chirality :  0.041   0.147    779
  Planarity :  0.005   0.046    817
  Dihedral  :  3.954  16.857    722
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.40 %
    Favored  : 84.80 %
  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:  2.09 (0.35), residues: 609
  helix:  2.02 (0.24), residues: 452
  sheet:  None (None), residues: 0
  loop : -0.45 (0.55), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 487 
 HIS   0.003   0.001   HIS A  80 
 PHE   0.009   0.001   PHE A 453 
 TYR   0.010   0.002   TYR A 290 
 ARG   0.003   0.000   ARG A 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04114 (  342)
  hydrogen bonds       : angle       5.29429 ( 1020)
  SS BOND              : bond        0.00236 (    4)
  SS BOND              : angle       0.76392 (    8)
  covalent geometry    : bond        0.00298 ( 4904)
  covalent geometry    : angle       0.60369 ( 6692)

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

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

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A   45 CYS cc_start: 0.7883 (m) cc_final: 0.7010 (p)
REVERT: A   46 ARG cc_start: 0.6143 (ttt90) cc_final: 0.5800 (ttt-90)
REVERT: A  281 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6795 (tt)
REVERT: A  300 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7372 (mmt180)
REVERT: A  349 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7439 (mp0)
REVERT: A  407 MET cc_start: 0.8748 (mmm) cc_final: 0.8532 (mmt)
REVERT: A  416 ARG cc_start: 0.7238 (mpt180) cc_final: 0.7003 (mtm180)
REVERT: A  451 GLN cc_start: 0.8251 (mt0) cc_final: 0.7885 (mt0)
REVERT: A  548 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7354 (p)
REVERT: A  568 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6306 (mt-10)
REVERT: A  661 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7718 (mtm)
  outliers start: 14
  outliers final: 5
  residues processed: 67
  average time/residue: 1.3119
  time to fit residues: 91.5218
Evaluate side-chains
  69 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  661 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 48 optimal weight:    0.1980
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   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 167 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.123327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.102540 restraints weight = 5090.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 1.31
r_work: 0.2937 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4908  Z= 0.115
  Angle     :  0.581  15.164   6700  Z= 0.284
  Chirality :  0.039   0.139    779
  Planarity :  0.005   0.045    817
  Dihedral  :  3.842  17.150    722
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 12.60 %
    Favored  : 84.80 %
  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:  2.26 (0.35), residues: 609
  helix:  2.14 (0.24), residues: 452
  sheet:  None (None), residues: 0
  loop : -0.41 (0.54), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 276 
 HIS   0.003   0.001   HIS A  80 
 PHE   0.014   0.001   PHE A 254 
 TYR   0.010   0.001   TYR A 188 
 ARG   0.004   0.000   ARG A 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03758 (  342)
  hydrogen bonds       : angle       5.15910 ( 1020)
  SS BOND              : bond        0.00193 (    4)
  SS BOND              : angle       0.71615 (    8)
  covalent geometry    : bond        0.00240 ( 4904)
  covalent geometry    : angle       0.58044 ( 6692)

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

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

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.494 
Fit side-chains
REVERT: A   45 CYS cc_start: 0.7824 (m) cc_final: 0.6901 (p)
REVERT: A   46 ARG cc_start: 0.6145 (ttt90) cc_final: 0.5823 (ttt-90)
REVERT: A  300 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7350 (mmt180)
REVERT: A  349 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7417 (mp0)
REVERT: A  407 MET cc_start: 0.8751 (mmm) cc_final: 0.8389 (mmt)
REVERT: A  451 GLN cc_start: 0.8217 (mt0) cc_final: 0.7948 (mt0)
REVERT: A  548 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7397 (p)
REVERT: A  568 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6233 (mt-10)
  outliers start: 13
  outliers final: 1
  residues processed: 72
  average time/residue: 1.2305
  time to fit residues: 91.9713
Evaluate side-chains
  64 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  548 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 55 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
** A 376 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 = 0.3279 r_free = 0.3279 target = 0.120567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.099459 restraints weight = 5177.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 1.29
r_work: 0.2897 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4908  Z= 0.136
  Angle     :  0.619  15.984   6700  Z= 0.303
  Chirality :  0.041   0.144    779
  Planarity :  0.005   0.047    817
  Dihedral  :  3.871  16.694    722
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.20 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.35), residues: 609
  helix:  2.10 (0.24), residues: 452
  sheet:  None (None), residues: 0
  loop : -0.37 (0.54), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 487 
 HIS   0.003   0.001   HIS A  80 
 PHE   0.009   0.001   PHE A 453 
 TYR   0.013   0.002   TYR A 188 
 ARG   0.003   0.000   ARG A 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04102 (  342)
  hydrogen bonds       : angle       5.24935 ( 1020)
  SS BOND              : bond        0.00223 (    4)
  SS BOND              : angle       0.72587 (    8)
  covalent geometry    : bond        0.00301 ( 4904)
  covalent geometry    : angle       0.61858 ( 6692)

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

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

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.534 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7883 (mtm) cc_final: 0.7645 (mtm)
REVERT: A   45 CYS cc_start: 0.7806 (m) cc_final: 0.6851 (p)
REVERT: A   46 ARG cc_start: 0.6158 (ttt90) cc_final: 0.5818 (ttt-90)
REVERT: A  300 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7327 (mmt180)
REVERT: A  349 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7399 (mp0)
REVERT: A  420 ARG cc_start: 0.7415 (ttm-80) cc_final: 0.7154 (ttp80)
REVERT: A  451 GLN cc_start: 0.8202 (mt0) cc_final: 0.7915 (mt0)
REVERT: A  548 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7328 (p)
REVERT: A  568 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6324 (mt-10)
  outliers start: 7
  outliers final: 1
  residues processed: 67
  average time/residue: 1.3248
  time to fit residues: 92.4486
Evaluate side-chains
  62 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  548 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 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 = 0.120724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.097884 restraints weight = 5068.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 1.43
r_work: 0.2872 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4908  Z= 0.143
  Angle     :  0.630  16.313   6700  Z= 0.308
  Chirality :  0.041   0.148    779
  Planarity :  0.005   0.048    817
  Dihedral  :  3.899  16.615    722
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.60 %
    Favored  : 83.80 %
  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:  2.18 (0.35), residues: 609
  helix:  2.05 (0.24), residues: 452
  sheet:  None (None), residues: 0
  loop : -0.31 (0.55), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 487 
 HIS   0.004   0.001   HIS A  80 
 PHE   0.009   0.001   PHE A 453 
 TYR   0.012   0.002   TYR A 188 
 ARG   0.003   0.000   ARG A 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04226 (  342)
  hydrogen bonds       : angle       5.30453 ( 1020)
  SS BOND              : bond        0.00239 (    4)
  SS BOND              : angle       0.74814 (    8)
  covalent geometry    : bond        0.00317 ( 4904)
  covalent geometry    : angle       0.63016 ( 6692)

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

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

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7809 (mtm) cc_final: 0.7544 (mtm)
REVERT: A   45 CYS cc_start: 0.7871 (m) cc_final: 0.6852 (p)
REVERT: A   46 ARG cc_start: 0.6054 (ttt90) cc_final: 0.5711 (ttt-90)
REVERT: A  300 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7232 (mmt180)
REVERT: A  349 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7291 (mp0)
REVERT: A  420 ARG cc_start: 0.7289 (ttm-80) cc_final: 0.7073 (ttp80)
REVERT: A  451 GLN cc_start: 0.8127 (mt0) cc_final: 0.7827 (mt0)
REVERT: A  548 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7204 (p)
REVERT: A  568 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6296 (mt-10)
  outliers start: 8
  outliers final: 3
  residues processed: 66
  average time/residue: 1.3991
  time to fit residues: 95.9552
Evaluate side-chains
  66 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  548 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 376 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.122986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.100495 restraints weight = 5111.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.41
r_work: 0.2919 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4908  Z= 0.121
  Angle     :  0.605  15.800   6700  Z= 0.294
  Chirality :  0.040   0.142    779
  Planarity :  0.005   0.046    817
  Dihedral  :  3.820  17.055    722
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 15.60 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.35), residues: 609
  helix:  2.14 (0.24), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.32 (0.54), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 276 
 HIS   0.003   0.001   HIS A  80 
 PHE   0.008   0.001   PHE A 534 
 TYR   0.013   0.001   TYR A 188 
 ARG   0.005   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  342)
  hydrogen bonds       : angle       5.17539 ( 1020)
  SS BOND              : bond        0.00201 (    4)
  SS BOND              : angle       0.75659 (    8)
  covalent geometry    : bond        0.00258 ( 4904)
  covalent geometry    : angle       0.60524 ( 6692)

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

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

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1218 Ramachandran restraints generated.
    609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7821 (mtm) cc_final: 0.7571 (mtm)
REVERT: A   45 CYS cc_start: 0.7801 (m) cc_final: 0.6675 (p)
REVERT: A   46 ARG cc_start: 0.6226 (ttt90) cc_final: 0.5817 (ttt-90)
REVERT: A   51 THR cc_start: 0.8559 (t) cc_final: 0.8127 (m)
REVERT: A  300 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7254 (mmt180)
REVERT: A  349 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7313 (mp0)
REVERT: A  451 GLN cc_start: 0.8135 (mt0) cc_final: 0.7881 (mt0)
REVERT: A  548 THR cc_start: 0.7526 (OUTLIER) cc_final: 0.7195 (p)
REVERT: A  568 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6258 (mt-10)
  outliers start: 6
  outliers final: 2
  residues processed: 64
  average time/residue: 1.2767
  time to fit residues: 84.8896
Evaluate side-chains
  64 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  548 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 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 = 0.3260 r_free = 0.3260 target = 0.118970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.096921 restraints weight = 5215.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 1.34
r_work: 0.2861 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4908  Z= 0.165
  Angle     :  0.666  16.686   6700  Z= 0.323
  Chirality :  0.043   0.161    779
  Planarity :  0.005   0.049    817
  Dihedral  :  3.957  16.275    722
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.80 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.10 (0.35), residues: 609
  helix:  1.96 (0.24), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.26 (0.55), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 429 
 HIS   0.004   0.001   HIS A  80 
 PHE   0.023   0.002   PHE A 254 
 TYR   0.014   0.002   TYR A 188 
 ARG   0.005   0.001   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04501 (  342)
  hydrogen bonds       : angle       5.38843 ( 1020)
  SS BOND              : bond        0.00280 (    4)
  SS BOND              : angle       0.76425 (    8)
  covalent geometry    : bond        0.00376 ( 4904)
  covalent geometry    : angle       0.66626 ( 6692)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3223.22 seconds
wall clock time: 56 minutes 12.21 seconds (3372.21 seconds total)