Starting phenix.real_space_refine
on Sun Apr 27 00:22:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v3s_42952/04_2025/8v3s_42952.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v3s_42952/04_2025/8v3s_42952.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v3s_42952/04_2025/8v3s_42952.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v3s_42952/04_2025/8v3s_42952.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v3s_42952/04_2025/8v3s_42952.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v3s_42952/04_2025/8v3s_42952.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      21      5.16       5
     C    2492      2.51       5
     N     697      2.21       5
     O     698      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3909
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 499, 3870
          Classifications: {'peptide': 499}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 35, 'TRANS': 463}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 166
          Unresolved non-hydrogen angles: 199
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 122
    Chain: "M"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 28
          Classifications: {'peptide': 5}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'TRANS': 4}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 4}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "M"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 4.38, per 1000 atoms: 1.12
  Number of scatterers: 3909
  At special positions: 0
  Unit cell: (80.925, 73.455, 69.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      21     16.00
     O     698      8.00
     N     697      7.00
     C    2492      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 452.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" ND1 HIS A 434 "
        pdb="ZN    ZN A 701 " - pdb=" ND1 HIS A 252 "


  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  948

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 5 sheets defined
      31.5% alpha, 17.2% 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 98 through 104
    Processing helix  chain 'A' and resid 160 through 175
    Processing helix  chain 'A' and resid 256 through 270
      removed outlier: 3.865A  pdb=" N   PHE A 260 " --> pdb=" O   THR A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 283
    Processing helix  chain 'A' and resid 293 through 299
    Processing helix  chain 'A' and resid 310 through 314
    Processing helix  chain 'A' and resid 323 through 340
    Processing helix  chain 'A' and resid 451 through 467
      removed outlier: 4.362A  pdb=" N   TYR A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
      Proline residue:  A 462  - end of helix
    Processing helix  chain 'A' and resid 481 through 486
      removed outlier: 3.844A  pdb=" N   TYR A 485 " --> pdb=" O   GLU A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 497
      removed outlier: 3.659A  pdb=" N   GLY A 497 " --> pdb=" O   SER A 494 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 494 through 497'
    Processing helix  chain 'A' and resid 498 through 508
    Processing helix  chain 'A' and resid 551 through 570
      removed outlier: 3.976A  pdb=" N   ALA A 570 " --> pdb=" O   ALA A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 581
    Processing helix  chain 'A' and resid 585 through 601
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5
      removed outlier: 5.232A  pdb=" N   THR A 112 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   ARG A 118 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.733A  pdb=" N   TYR A  52 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   ASN A  91 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   PHE A  54 " --> pdb=" O   ASN A  91 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 128
    Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 198
      removed outlier: 7.153A  pdb=" N   VAL A 205 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   PHE A 245 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   ILE A 289 " --> pdb=" O   PHE A 245 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU A 247 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE A 244 " --> pdb=" O   TYR A 429 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   VAL A 431 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   PHE A 246 " --> pdb=" O   VAL A 431 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   LEU A 433 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 433 " (cutoff:3.500A)
      removed outlier: 9.218A  pdb=" N   GLY A 435 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 220
      removed outlier: 5.843A  pdb=" N   ASP A 219 " --> pdb=" O   ARG A 238 " (cutoff:3.500A)

    145 hydrogen bonds defined for protein.
    408 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: 1.03

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 713
        1.31 -     1.44: 1089
        1.44 -     1.57: 2182
        1.57 -     1.69: 4
        1.69 -     1.82: 31
  Bond restraints: 4019
  Sorted by residual:
  bond pdb=" N   GLU M1001 "
       pdb=" CA  GLU M1001 "
    ideal  model  delta    sigma   weight residual
    1.458  1.525 -0.067 1.90e-02 2.77e+03 1.23e+01
  bond pdb=" CZ  ARG A 276 "
       pdb=" NH2 ARG A 276 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.10e+00
  bond pdb=" CA  GLU M1001 "
       pdb=" C   GLU M1001 "
    ideal  model  delta    sigma   weight residual
    1.525  1.588 -0.063 2.10e-02 2.27e+03 9.04e+00
  bond pdb=" CZ  ARG A 250 "
       pdb=" NH2 ARG A 250 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 8.96e+00
  bond pdb=" CZ  ARG A 238 "
       pdb=" NH2 ARG A 238 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.40e+00
  ... (remaining 4014 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 3959
        1.50 -     2.99: 1199
        2.99 -     4.48: 242
        4.48 -     5.98: 48
        5.98 -     7.47: 16
  Bond angle restraints: 5464
  Sorted by residual:
  angle pdb=" N   ILE A 578 "
        pdb=" CA  ILE A 578 "
        pdb=" C   ILE A 578 "
      ideal   model   delta    sigma   weight residual
     110.62  116.35   -5.73 1.02e+00 9.61e-01 3.16e+01
  angle pdb=" C   SER A 539 "
        pdb=" N   PRO A 540 "
        pdb=" CA  PRO A 540 "
      ideal   model   delta    sigma   weight residual
     119.66  115.66    4.00 7.20e-01 1.93e+00 3.09e+01
  angle pdb=" C   ALA A 545 "
        pdb=" CA  ALA A 545 "
        pdb=" CB  ALA A 545 "
      ideal   model   delta    sigma   weight residual
     116.54  110.26    6.28 1.15e+00 7.56e-01 2.98e+01
  angle pdb=" C   SER A 548 "
        pdb=" CA  SER A 548 "
        pdb=" CB  SER A 548 "
      ideal   model   delta    sigma   weight residual
     117.23  110.47    6.76 1.36e+00 5.41e-01 2.47e+01
  angle pdb=" OE1 GLN A 475 "
        pdb=" CD  GLN A 475 "
        pdb=" NE2 GLN A 475 "
      ideal   model   delta    sigma   weight residual
     122.60  117.71    4.89 1.00e+00 1.00e+00 2.39e+01
  ... (remaining 5459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 2194
       17.82 -    35.65: 145
       35.65 -    53.47: 25
       53.47 -    71.30: 5
       71.30 -    89.12: 3
  Dihedral angle restraints: 2372
    sinusoidal: 904
      harmonic: 1468
  Sorted by residual:
  dihedral pdb=" CA  TYR A 519 "
           pdb=" C   TYR A 519 "
           pdb=" N   ASN A 520 "
           pdb=" CA  ASN A 520 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.40  -19.60     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  HIS A 583 "
           pdb=" C   HIS A 583 "
           pdb=" N   SER A 584 "
           pdb=" CA  SER A 584 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.31  -18.69     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  ARG A  72 "
           pdb=" C   ARG A  72 "
           pdb=" N   SER A  73 "
           pdb=" CA  SER A  73 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.51  -18.49     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 2369 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 375
       0.067 -    0.133: 130
       0.133 -    0.200: 60
       0.200 -    0.266: 14
       0.266 -    0.333: 6
  Chirality restraints: 585
  Sorted by residual:
  chirality pdb=" CA  SER A  16 "
            pdb=" N   SER A  16 "
            pdb=" C   SER A  16 "
            pdb=" CB  SER A  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CA  GLU M1001 "
            pdb=" N   GLU M1001 "
            pdb=" C   GLU M1001 "
            pdb=" CB  GLU M1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CA  GLU M   3 "
            pdb=" N   GLU M   3 "
            pdb=" C   GLU M   3 "
            pdb=" CB  GLU M   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.35e+00
  ... (remaining 582 not shown)

  Planarity restraints: 718
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 519 "    0.050 2.00e-02 2.50e+03   2.65e-02 1.40e+01
        pdb=" CG  TYR A 519 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 519 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 519 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 519 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 519 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 519 "   -0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR A 519 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 192 "    0.037 2.00e-02 2.50e+03   2.90e-02 1.26e+01
        pdb=" CG  HIS A 192 "   -0.046 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 192 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 192 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 192 "    0.005 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 192 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 335 "   -0.039 2.00e-02 2.50e+03   2.49e-02 1.24e+01
        pdb=" CG  TYR A 335 "    0.009 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 335 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 335 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 335 "    0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 335 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 335 "    0.013 2.00e-02 2.50e+03
        pdb=" OH  TYR A 335 "   -0.046 2.00e-02 2.50e+03
  ... (remaining 715 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 5
        2.56 -     3.15: 3042
        3.15 -     3.73: 6284
        3.73 -     4.32: 8769
        4.32 -     4.90: 14492
  Nonbonded interactions: 32592
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 255 "
            pdb="ZN    ZN A 701 "
     model   vdw
     1.978 2.230
  nonbonded pdb=" OE2 GLU A 255 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.097 2.230
  nonbonded pdb=" CD  GLU A 255 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.263 2.460
  nonbonded pdb=" OG1 THR A 521 "
            pdb=" O   SER A 548 "
     model   vdw
     2.480 3.040
  nonbonded pdb=" O   ASN A 458 "
            pdb=" OH  TYR A 513 "
     model   vdw
     2.555 3.040
  ... (remaining 32587 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.690
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.820
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
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      :  0.013   0.257   4022  Z= 0.726
  Angle     :  1.522   7.475   5464  Z= 1.003
  Chirality :  0.086   0.333    585
  Planarity :  0.011   0.067    718
  Dihedral  : 12.860  89.124   1424
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.44 %
    Favored  : 91.56 %
  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: -1.14 (0.33), residues: 491
  helix: -0.47 (0.35), residues: 143
  sheet: -0.15 (0.58), residues: 72
  loop : -1.05 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.008   TRP A 575 
 HIS   0.018   0.006   HIS A 436 
 PHE   0.036   0.006   PHE A 265 
 TYR   0.050   0.012   TYR A 519 
 ARG   0.016   0.002   ARG A  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17478 (  145)
  hydrogen bonds       : angle       7.73599 (  408)
  metal coordination   : bond        0.24871 (    2)
  covalent geometry    : bond        0.01142 ( 4019)
  covalent geometry    : angle       1.52219 ( 5464)
  Misc. bond           : bond        0.04527 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8260 (mt) cc_final: 0.8056 (mm)
REVERT: A   52 TYR cc_start: 0.7967 (m-80) cc_final: 0.7673 (m-10)
REVERT: A   69 ASN cc_start: 0.7676 (t0) cc_final: 0.7414 (t0)
REVERT: A  307 ARG cc_start: 0.7254 (ttp80) cc_final: 0.6802 (ttp-170)
REVERT: A  521 THR cc_start: 0.8097 (t) cc_final: 0.7822 (m)
REVERT: A  557 GLN cc_start: 0.7552 (tp-100) cc_final: 0.6999 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1813
  time to fit residues: 15.5439
Evaluate side-chains
  38 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:    0.1980
   chunk 37 optimal weight:    0.0770
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0980
   chunk 25 optimal weight:    0.0980
   chunk 19 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0970
   chunk 23 optimal weight:    0.0980
   chunk 28 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.0936

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

Flipped N/Q/H residues before XYZ refinement:
A 599 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.131647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.120221 restraints weight = 5901.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.123094 restraints weight = 3341.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.125037 restraints weight = 2208.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4022  Z= 0.117
  Angle     :  0.609  12.572   5464  Z= 0.307
  Chirality :  0.042   0.140    585
  Planarity :  0.005   0.042    718
  Dihedral  :  4.910  49.094    557
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.17 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.36), residues: 491
  helix:  0.81 (0.40), residues: 143
  sheet:  0.21 (0.58), residues: 72
  loop : -0.70 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  57 
 HIS   0.004   0.001   HIS A 596 
 PHE   0.016   0.001   PHE A 265 
 TYR   0.018   0.002   TYR A 461 
 ARG   0.008   0.001   ARG A 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04428 (  145)
  hydrogen bonds       : angle       5.70811 (  408)
  metal coordination   : bond        0.00298 (    2)
  covalent geometry    : bond        0.00258 ( 4019)
  covalent geometry    : angle       0.60856 ( 5464)
  Misc. bond           : bond        0.00023 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.473 
Fit side-chains
REVERT: A  557 GLN cc_start: 0.8158 (tp-100) cc_final: 0.7905 (tp-100)
  outliers start: 7
  outliers final: 6
  residues processed: 50
  average time/residue: 0.1845
  time to fit residues: 11.6316
Evaluate side-chains
  41 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  578 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0970
   chunk 9 optimal weight:    0.2980
   chunk 46 optimal weight:    0.0980
   chunk 28 optimal weight:    0.4980
   overall best weight:    0.3178

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.124695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.112700 restraints weight = 6002.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.115477 restraints weight = 3479.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.117331 restraints weight = 2349.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   4022  Z= 0.201
  Angle     :  0.637  10.858   5464  Z= 0.324
  Chirality :  0.044   0.191    585
  Planarity :  0.005   0.047    718
  Dihedral  :  5.018  51.093    557
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 12.90 %
    Favored  : 84.12 %
  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: -0.13 (0.36), residues: 491
  helix:  0.93 (0.41), residues: 143
  sheet:  0.06 (0.55), residues: 77
  loop : -0.65 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A 596 
 PHE   0.011   0.002   PHE A 268 
 TYR   0.025   0.002   TYR A 161 
 ARG   0.015   0.001   ARG A 598 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04416 (  145)
  hydrogen bonds       : angle       5.31712 (  408)
  metal coordination   : bond        0.00570 (    2)
  covalent geometry    : bond        0.00482 ( 4019)
  covalent geometry    : angle       0.63738 ( 5464)
  Misc. bond           : bond        0.00104 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A  150 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8200 (p)
REVERT: A  557 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8244 (tp-100)
  outliers start: 12
  outliers final: 9
  residues processed: 49
  average time/residue: 0.1390
  time to fit residues: 9.0527
Evaluate side-chains
  41 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  444 MET
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  578 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 28 optimal weight:    0.1980
   chunk 48 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0670
   chunk 40 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0980
   chunk 30 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0770
   chunk 33 optimal weight:    0.2980
   chunk 1 optimal weight:    0.0970
   chunk 36 optimal weight:    0.1980
   overall best weight:    0.1074

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

Flipped N/Q/H residues before XYZ refinement:
A 336 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.125169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.112942 restraints weight = 6006.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.115696 restraints weight = 3372.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.117790 restraints weight = 2280.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4022  Z= 0.103
  Angle     :  0.547  10.451   5464  Z= 0.272
  Chirality :  0.040   0.130    585
  Planarity :  0.004   0.047    718
  Dihedral  :  4.755  53.645    557
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.63 %
    Favored  : 81.64 %
  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 (0.37), residues: 491
  helix:  1.12 (0.41), residues: 143
  sheet:  0.22 (0.56), residues: 77
  loop : -0.62 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 119 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.014   0.001   PHE A 286 
 TYR   0.020   0.001   TYR A 161 
 ARG   0.005   0.000   ARG A 598 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03571 (  145)
  hydrogen bonds       : angle       5.00413 (  408)
  metal coordination   : bond        0.00197 (    2)
  covalent geometry    : bond        0.00240 ( 4019)
  covalent geometry    : angle       0.54718 ( 5464)
  Misc. bond           : bond        0.00037 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  191 TYR cc_start: 0.7537 (t80) cc_final: 0.7325 (t80)
REVERT: A  459 MET cc_start: 0.8158 (mtt) cc_final: 0.7888 (mtp)
REVERT: A  557 GLN cc_start: 0.8384 (tp-100) cc_final: 0.8020 (tp-100)
  outliers start: 11
  outliers final: 7
  residues processed: 48
  average time/residue: 0.1380
  time to fit residues: 8.7612
Evaluate side-chains
  42 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  578 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   chunk 15 optimal weight:    0.2980
   chunk 16 optimal weight:    0.0870
   chunk 19 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0570
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   chunk 33 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0970
   overall best weight:    0.1674

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.123187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.111352 restraints weight = 6160.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.114116 restraints weight = 3584.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.115981 restraints weight = 2432.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4022  Z= 0.125
  Angle     :  0.554   9.833   5464  Z= 0.277
  Chirality :  0.041   0.127    585
  Planarity :  0.004   0.046    718
  Dihedral  :  4.719  53.928    557
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 14.64 %
    Favored  : 81.64 %
  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:  0.09 (0.37), residues: 491
  helix:  1.19 (0.41), residues: 144
  sheet:  0.52 (0.56), residues: 85
  loop : -0.73 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 119 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.020   0.001   PHE A 135 
 TYR   0.017   0.001   TYR A 161 
 ARG   0.004   0.000   ARG A 598 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03523 (  145)
  hydrogen bonds       : angle       4.94118 (  408)
  metal coordination   : bond        0.00259 (    2)
  covalent geometry    : bond        0.00298 ( 4019)
  covalent geometry    : angle       0.55372 ( 5464)
  Misc. bond           : bond        0.00052 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 36
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  191 TYR cc_start: 0.7483 (t80) cc_final: 0.7263 (t80)
REVERT: A  459 MET cc_start: 0.8172 (mtt) cc_final: 0.7924 (mtt)
REVERT: A  557 GLN cc_start: 0.8499 (tp-100) cc_final: 0.8138 (tp-100)
REVERT: A  593 MET cc_start: 0.8092 (tpp) cc_final: 0.7888 (tpp)
  outliers start: 15
  outliers final: 10
  residues processed: 49
  average time/residue: 0.1596
  time to fit residues: 10.5612
Evaluate side-chains
  43 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  456 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0870
   chunk 33 optimal weight:    0.0970
   chunk 19 optimal weight:    0.0040
   chunk 25 optimal weight:    0.1980
   chunk 11 optimal weight:    0.3980
   chunk 22 optimal weight:    0.0980
   chunk 18 optimal weight:    0.2980
   chunk 13 optimal weight:    0.0980
   overall best weight:    0.0768

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.125390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.113642 restraints weight = 5991.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.116459 restraints weight = 3516.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.118336 restraints weight = 2380.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4022  Z= 0.095
  Angle     :  0.529   9.142   5464  Z= 0.263
  Chirality :  0.039   0.131    585
  Planarity :  0.004   0.048    718
  Dihedral  :  4.535  52.855    557
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.24 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.63 %
    Favored  : 81.64 %
  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:  0.29 (0.37), residues: 491
  helix:  1.45 (0.42), residues: 144
  sheet:  0.70 (0.56), residues: 85
  loop : -0.70 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  57 
 HIS   0.002   0.001   HIS A 323 
 PHE   0.011   0.001   PHE A 135 
 TYR   0.016   0.001   TYR A 161 
 ARG   0.004   0.000   ARG A 598 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03126 (  145)
  hydrogen bonds       : angle       4.84517 (  408)
  metal coordination   : bond        0.00154 (    2)
  covalent geometry    : bond        0.00225 ( 4019)
  covalent geometry    : angle       0.52936 ( 5464)
  Misc. bond           : bond        0.00023 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.599 
Fit side-chains
REVERT: A  106 MET cc_start: 0.8574 (tpt) cc_final: 0.8132 (tpt)
REVERT: A  191 TYR cc_start: 0.7455 (t80) cc_final: 0.7190 (t80)
REVERT: A  459 MET cc_start: 0.8219 (mtt) cc_final: 0.7984 (mtt)
REVERT: A  593 MET cc_start: 0.8056 (tpp) cc_final: 0.7832 (tpp)
REVERT: A  595 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8377 (mtmm)
  outliers start: 11
  outliers final: 10
  residues processed: 45
  average time/residue: 0.1706
  time to fit residues: 10.4936
Evaluate side-chains
  44 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  583 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0980
   chunk 33 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 45 optimal weight:    0.2980
   chunk 31 optimal weight:    0.0770
   chunk 22 optimal weight:    0.0980
   chunk 14 optimal weight:    0.8980
   chunk 21 optimal weight:    0.4980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.2138

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.108845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.095235 restraints weight = 6362.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.098101 restraints weight = 3742.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.100038 restraints weight = 2561.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4022  Z= 0.142
  Angle     :  0.554   8.616   5464  Z= 0.278
  Chirality :  0.040   0.130    585
  Planarity :  0.004   0.047    718
  Dihedral  :  4.595  51.871    557
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.05 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.89 %
    Favored  : 81.89 %
  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:  0.30 (0.37), residues: 491
  helix:  1.36 (0.42), residues: 144
  sheet:  0.85 (0.57), residues: 85
  loop : -0.69 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.010   0.001   PHE A 135 
 TYR   0.015   0.002   TYR A 161 
 ARG   0.003   0.000   ARG A 598 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03552 (  145)
  hydrogen bonds       : angle       4.87832 (  408)
  metal coordination   : bond        0.00309 (    2)
  covalent geometry    : bond        0.00343 ( 4019)
  covalent geometry    : angle       0.55355 ( 5464)
  Misc. bond           : bond        0.00057 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.8379 (mt0) cc_final: 0.8004 (mt0)
REVERT: A  130 MET cc_start: 0.6153 (tpt) cc_final: 0.5819 (tpt)
REVERT: A  191 TYR cc_start: 0.7785 (t80) cc_final: 0.7500 (t80)
REVERT: A  314 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7367 (mm-40)
REVERT: A  459 MET cc_start: 0.8455 (mtt) cc_final: 0.8196 (mtt)
REVERT: A  593 MET cc_start: 0.8088 (tpp) cc_final: 0.7849 (tpp)
REVERT: A  595 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8280 (mtmm)
  outliers start: 13
  outliers final: 12
  residues processed: 48
  average time/residue: 0.2846
  time to fit residues: 18.5347
Evaluate side-chains
  49 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  583 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 45 optimal weight:    0.0980
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    0.4980
   chunk 1 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0970
   chunk 35 optimal weight:    0.3980
   chunk 36 optimal weight:    0.3980
   chunk 0 optimal weight:    0.9990
   chunk 8 optimal weight:    0.2980
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.2378

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 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 = 0.3284 r_free = 0.3284 target = 0.104282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.090436 restraints weight = 6476.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.093153 restraints weight = 3854.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.095130 restraints weight = 2676.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4022  Z= 0.153
  Angle     :  0.559   8.302   5464  Z= 0.282
  Chirality :  0.041   0.128    585
  Planarity :  0.004   0.048    718
  Dihedral  :  4.618  50.503    557
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.65 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 13.15 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.28 (0.37), residues: 491
  helix:  1.46 (0.42), residues: 138
  sheet:  0.94 (0.56), residues: 85
  loop : -0.76 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  57 
 HIS   0.004   0.001   HIS A 336 
 PHE   0.010   0.001   PHE A 139 
 TYR   0.016   0.002   TYR A 161 
 ARG   0.003   0.000   ARG A 598 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03628 (  145)
  hydrogen bonds       : angle       4.93427 (  408)
  metal coordination   : bond        0.00351 (    2)
  covalent geometry    : bond        0.00368 ( 4019)
  covalent geometry    : angle       0.55929 ( 5464)
  Misc. bond           : bond        0.00055 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 36
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A  130 MET cc_start: 0.6394 (tpt) cc_final: 0.6137 (tpt)
REVERT: A  314 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7437 (mm-40)
REVERT: A  440 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8091 (mtm180)
REVERT: A  459 MET cc_start: 0.8492 (mtt) cc_final: 0.8206 (mtt)
REVERT: A  593 MET cc_start: 0.8109 (tpp) cc_final: 0.7867 (tpp)
  outliers start: 18
  outliers final: 14
  residues processed: 53
  average time/residue: 0.2133
  time to fit residues: 14.7119
Evaluate side-chains
  47 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 32
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  440 ARG
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  583 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 29 optimal weight:    0.2980
   chunk 31 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0980
   chunk 39 optimal weight:    0.1980
   chunk 40 optimal weight:    0.0770
   chunk 10 optimal weight:    0.7980
   chunk 46 optimal weight:    0.3980
   overall best weight:    0.2138

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.105005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.091303 restraints weight = 6485.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.094081 restraints weight = 3820.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.095935 restraints weight = 2627.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4022  Z= 0.145
  Angle     :  0.573   8.175   5464  Z= 0.287
  Chirality :  0.041   0.137    585
  Planarity :  0.004   0.048    718
  Dihedral  :  4.564  47.348    557
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.44 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 14.14 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.37), residues: 491
  helix:  1.46 (0.42), residues: 138
  sheet:  0.97 (0.56), residues: 85
  loop : -0.81 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  57 
 HIS   0.004   0.001   HIS A 336 
 PHE   0.010   0.001   PHE A 139 
 TYR   0.015   0.002   TYR A 161 
 ARG   0.006   0.001   ARG A 537 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03569 (  145)
  hydrogen bonds       : angle       4.93069 (  408)
  metal coordination   : bond        0.00316 (    2)
  covalent geometry    : bond        0.00351 ( 4019)
  covalent geometry    : angle       0.57309 ( 5464)
  Misc. bond           : bond        0.00048 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 35
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A  130 MET cc_start: 0.6487 (tpt) cc_final: 0.6284 (tpt)
REVERT: A  191 TYR cc_start: 0.7781 (t80) cc_final: 0.7379 (t80)
REVERT: A  314 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7445 (mm-40)
REVERT: A  459 MET cc_start: 0.8496 (mtt) cc_final: 0.8210 (mtt)
REVERT: A  593 MET cc_start: 0.8102 (tpp) cc_final: 0.7875 (tpp)
REVERT: A  595 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8333 (mtmm)
  outliers start: 15
  outliers final: 14
  residues processed: 49
  average time/residue: 0.1299
  time to fit residues: 8.5862
Evaluate side-chains
  47 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 33
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  583 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 4 optimal weight:    0.2980
   chunk 33 optimal weight:    0.0870
   chunk 17 optimal weight:    0.4980
   chunk 45 optimal weight:    0.0970
   chunk 12 optimal weight:    0.9990
   chunk 36 optimal weight:    0.2980
   chunk 34 optimal weight:    0.0970
   chunk 41 optimal weight:    0.0970
   chunk 29 optimal weight:    0.1980
   chunk 27 optimal weight:    0.0970
   overall best weight:    0.0950

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.106855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.093245 restraints weight = 6423.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.096073 restraints weight = 3744.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.098022 restraints weight = 2562.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4022  Z= 0.104
  Angle     :  0.546   7.859   5464  Z= 0.271
  Chirality :  0.040   0.132    585
  Planarity :  0.004   0.050    718
  Dihedral  :  4.370  43.582    557
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.83 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.14 %
    Favored  : 82.13 %
  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:  0.39 (0.37), residues: 491
  helix:  1.37 (0.42), residues: 144
  sheet:  1.14 (0.57), residues: 85
  loop : -0.68 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  57 
 HIS   0.003   0.001   HIS A 434 
 PHE   0.008   0.001   PHE A  54 
 TYR   0.015   0.001   TYR A 161 
 ARG   0.008   0.001   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03177 (  145)
  hydrogen bonds       : angle       4.80647 (  408)
  metal coordination   : bond        0.00181 (    2)
  covalent geometry    : bond        0.00251 ( 4019)
  covalent geometry    : angle       0.54603 ( 5464)
  Misc. bond           : bond        0.00020 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A  106 MET cc_start: 0.8591 (tpt) cc_final: 0.8029 (tpt)
REVERT: A  130 MET cc_start: 0.6446 (tpt) cc_final: 0.6221 (tpt)
REVERT: A  191 TYR cc_start: 0.7682 (t80) cc_final: 0.7295 (t80)
REVERT: A  314 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7445 (mm-40)
REVERT: A  459 MET cc_start: 0.8541 (mtt) cc_final: 0.8214 (mtt)
REVERT: A  593 MET cc_start: 0.8062 (tpp) cc_final: 0.7843 (tpp)
REVERT: A  595 LYS cc_start: 0.8868 (mtpp) cc_final: 0.8362 (mtmm)
  outliers start: 11
  outliers final: 11
  residues processed: 47
  average time/residue: 0.1595
  time to fit residues: 10.0385
Evaluate side-chains
  46 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  583 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0980
   chunk 4 optimal weight:    0.2980
   chunk 18 optimal weight:    0.0980
   chunk 33 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0980
   chunk 23 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0870
   chunk 37 optimal weight:    0.1980
   chunk 5 optimal weight:    0.0020
   chunk 15 optimal weight:    0.4980
   overall best weight:    0.0766

-------------------------------------------------------------------------------
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 = 0.3365 r_free = 0.3365 target = 0.109823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.096537 restraints weight = 6261.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.099402 restraints weight = 3655.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.101271 restraints weight = 2487.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4022  Z= 0.100
  Angle     :  0.544   8.126   5464  Z= 0.269
  Chirality :  0.039   0.138    585
  Planarity :  0.004   0.050    718
  Dihedral  :  4.224  39.226    557
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.24 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.39 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.47 (0.38), residues: 491
  helix:  1.42 (0.42), residues: 144
  sheet:  1.31 (0.59), residues: 85
  loop : -0.67 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  57 
 HIS   0.002   0.001   HIS A 434 
 PHE   0.007   0.001   PHE A  54 
 TYR   0.016   0.001   TYR A 161 
 ARG   0.009   0.001   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03182 (  145)
  hydrogen bonds       : angle       4.75989 (  408)
  metal coordination   : bond        0.00132 (    2)
  covalent geometry    : bond        0.00238 ( 4019)
  covalent geometry    : angle       0.54442 ( 5464)
  Misc. bond           : bond        0.00016 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2649.76 seconds
wall clock time: 47 minutes 58.32 seconds (2878.32 seconds total)