Starting phenix.real_space_refine
on Fri May  9 21:47:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v3s_42952/05_2025/8v3s_42952.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v3s_42952/05_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_42952/05_2025/8v3s_42952.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v3s_42952/05_2025/8v3s_42952.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v3s_42952/05_2025/8v3s_42952.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v3s_42952/05_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-5687/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: 3.84, per 1000 atoms: 0.98
  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: 1.05
  Conformation dependent library (CDL) restraints added in 511.1 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: 0.55
  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: 1.05

  Time building geometry restraints manager: 1.21 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:             5.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.950
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.240
-------------------------------------------------------------------------------
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  : 0.421 
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: 0.1826
  time to fit residues: 15.6772
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  : 0.423 
-------------------------------------------------------------------------------
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 = 40)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.120218 restraints weight = 5901.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.123100 restraints weight = 3338.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.124990 restraints weight = 2207.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
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  : 0.427 
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: 0.1703
  time to fit residues: 10.7336
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  : 0.415 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0870
   chunk 9 optimal weight:    0.2980
   chunk 46 optimal weight:    0.0980
   chunk 28 optimal weight:    0.2980
   overall best weight:    0.2758

-------------------------------------------------------------------------------
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**
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.123433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.111417 restraints weight = 5938.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.114215 restraints weight = 3352.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.116125 restraints weight = 2240.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2533

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= 0.182
  Angle     :  0.623  10.835   5464  Z= 0.316
  Chirality :  0.044   0.173    585
  Planarity :  0.005   0.046    718
  Dihedral  :  5.001  50.679    557
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 13.40 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.36), residues: 491
  helix:  1.00 (0.41), residues: 143
  sheet:  0.08 (0.55), residues: 77
  loop : -0.64 (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 192 
 PHE   0.012   0.002   PHE A 268 
 TYR   0.027   0.002   TYR A 161 
 ARG   0.015   0.001   ARG A 598 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04254 (  145)
  hydrogen bonds       : angle       5.25412 (  408)
  metal coordination   : bond        0.00422 (    2)
  covalent geometry    : bond        0.00431 ( 4019)
  covalent geometry    : angle       0.62318 ( 5464)
  Misc. bond           : bond        0.00095 (    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
  49 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.409 
Fit side-chains
REVERT: A  557 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8214 (tp-100)
REVERT: A  595 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8221 (mtmm)
  outliers start: 11
  outliers final: 9
  residues processed: 47
  average time/residue: 0.1661
  time to fit residues: 10.1472
Evaluate side-chains
  40 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0870
   chunk 30 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0980
   chunk 33 optimal weight:    0.3980
   chunk 1 optimal weight:    0.0980
   chunk 36 optimal weight:    0.0970
   overall best weight:    0.0954

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.125586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.113835 restraints weight = 5998.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.116596 restraints weight = 3501.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.118489 restraints weight = 2372.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4022  Z= 0.100
  Angle     :  0.539  10.469   5464  Z= 0.268
  Chirality :  0.040   0.130    585
  Planarity :  0.004   0.047    718
  Dihedral  :  4.701  52.791    557
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.38 %
    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:  0.06 (0.37), residues: 491
  helix:  1.24 (0.41), residues: 143
  sheet:  0.24 (0.57), residues: 77
  loop : -0.66 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A  57 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.013   0.001   PHE A 286 
 TYR   0.018   0.001   TYR A 161 
 ARG   0.005   0.000   ARG A 598 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03454 (  145)
  hydrogen bonds       : angle       4.97462 (  408)
  metal coordination   : bond        0.00218 (    2)
  covalent geometry    : bond        0.00234 ( 4019)
  covalent geometry    : angle       0.53902 ( 5464)
  Misc. bond           : bond        0.00034 (    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
  50 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.477 
Fit side-chains
REVERT: A  191 TYR cc_start: 0.7474 (t80) cc_final: 0.7246 (t80)
REVERT: A  557 GLN cc_start: 0.8349 (tp-100) cc_final: 0.8001 (tp-100)
  outliers start: 11
  outliers final: 6
  residues processed: 49
  average time/residue: 0.1600
  time to fit residues: 10.2305
Evaluate side-chains
  40 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    0.9990
   chunk 2 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0970
   chunk 16 optimal weight:    0.0980
   chunk 19 optimal weight:    0.9990
   chunk 3 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0870
   chunk 33 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0870
   overall best weight:    0.1134

-------------------------------------------------------------------------------
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**
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 = 0.125022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.113186 restraints weight = 6122.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.115963 restraints weight = 3553.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.117842 restraints weight = 2410.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2879

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= 0.107
  Angle     :  0.541   9.750   5464  Z= 0.270
  Chirality :  0.040   0.134    585
  Planarity :  0.004   0.048    718
  Dihedral  :  4.620  52.468    557
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    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:  0.13 (0.37), residues: 491
  helix:  1.29 (0.41), residues: 144
  sheet:  0.54 (0.56), residues: 85
  loop : -0.76 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.019   0.001   PHE A 135 
 TYR   0.016   0.001   TYR A 161 
 ARG   0.003   0.000   ARG A 598 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03340 (  145)
  hydrogen bonds       : angle       4.89489 (  408)
  metal coordination   : bond        0.00203 (    2)
  covalent geometry    : bond        0.00252 ( 4019)
  covalent geometry    : angle       0.54135 ( 5464)
  Misc. bond           : bond        0.00038 (    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: 13
    poor density    : 38
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A  106 MET cc_start: 0.8582 (tpt) cc_final: 0.8176 (tpt)
REVERT: A  191 TYR cc_start: 0.7466 (t80) cc_final: 0.7202 (t80)
REVERT: A  459 MET cc_start: 0.8201 (mtt) cc_final: 0.7879 (mtp)
REVERT: A  557 GLN cc_start: 0.8353 (tp-100) cc_final: 0.8003 (tp-100)
REVERT: A  593 MET cc_start: 0.8063 (tpp) cc_final: 0.7835 (tpp)
  outliers start: 13
  outliers final: 9
  residues processed: 50
  average time/residue: 0.1261
  time to fit residues: 8.5765
Evaluate side-chains
  43 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
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  233 THR
Chi-restraints excluded: chain A residue  321 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:    0.3980
   chunk 38 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0270
   chunk 33 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0060
   chunk 25 optimal weight:    0.0980
   chunk 11 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0970
   chunk 18 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.1252

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.124458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.112671 restraints weight = 5994.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.115455 restraints weight = 3524.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.117316 restraints weight = 2401.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3073

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= 0.109
  Angle     :  0.531   9.095   5464  Z= 0.265
  Chirality :  0.040   0.127    585
  Planarity :  0.004   0.048    718
  Dihedral  :  4.549  51.665    557
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.65 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.88 %
    Favored  : 81.14 %
  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:  0.24 (0.37), residues: 491
  helix:  1.40 (0.42), residues: 144
  sheet:  0.73 (0.56), residues: 85
  loop : -0.75 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  57 
 HIS   0.004   0.001   HIS A 323 
 PHE   0.011   0.001   PHE A 135 
 TYR   0.015   0.001   TYR A 161 
 ARG   0.004   0.000   ARG A 598 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03249 (  145)
  hydrogen bonds       : angle       4.82274 (  408)
  metal coordination   : bond        0.00223 (    2)
  covalent geometry    : bond        0.00259 ( 4019)
  covalent geometry    : angle       0.53091 ( 5464)
  Misc. bond           : bond        0.00036 (    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
  49 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A  130 MET cc_start: 0.5840 (tpt) cc_final: 0.5571 (tpt)
REVERT: A  191 TYR cc_start: 0.7457 (t80) cc_final: 0.7181 (t80)
REVERT: A  459 MET cc_start: 0.8213 (mtt) cc_final: 0.7953 (mtt)
REVERT: A  557 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8024 (tp-100)
REVERT: A  593 MET cc_start: 0.8050 (tpp) cc_final: 0.7817 (tpp)
REVERT: A  595 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8286 (mtmm)
  outliers start: 12
  outliers final: 11
  residues processed: 48
  average time/residue: 0.1407
  time to fit residues: 8.9334
Evaluate side-chains
  48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
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  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:    0.0070
   chunk 30 optimal weight:    0.1980
   chunk 33 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 45 optimal weight:    0.3980
   chunk 31 optimal weight:    0.2980
   chunk 22 optimal weight:    0.0980
   chunk 14 optimal weight:    0.8980
   chunk 21 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0770
   overall best weight:    0.1356

-------------------------------------------------------------------------------
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 = 0.3357 r_free = 0.3357 target = 0.109460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.095792 restraints weight = 6358.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.098667 restraints weight = 3681.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.100666 restraints weight = 2503.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3264

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= 0.111
  Angle     :  0.529   8.456   5464  Z= 0.264
  Chirality :  0.040   0.128    585
  Planarity :  0.004   0.049    718
  Dihedral  :  4.442  49.603    557
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.04 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.88 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.37), residues: 491
  helix:  1.44 (0.42), residues: 144
  sheet:  0.94 (0.58), residues: 85
  loop : -0.67 (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 336 
 PHE   0.009   0.001   PHE A  54 
 TYR   0.015   0.001   TYR A 161 
 ARG   0.002   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03229 (  145)
  hydrogen bonds       : angle       4.78185 (  408)
  metal coordination   : bond        0.00239 (    2)
  covalent geometry    : bond        0.00266 ( 4019)
  covalent geometry    : angle       0.52870 ( 5464)
  Misc. bond           : bond        0.00040 (    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: 12
    poor density    : 37
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.8349 (mt0) cc_final: 0.7974 (mt0)
REVERT: A  130 MET cc_start: 0.6268 (tpt) cc_final: 0.6052 (tpt)
REVERT: A  191 TYR cc_start: 0.7765 (t80) cc_final: 0.7419 (t80)
REVERT: A  459 MET cc_start: 0.8499 (mtt) cc_final: 0.8225 (mtt)
REVERT: A  593 MET cc_start: 0.8124 (tpp) cc_final: 0.7872 (tpp)
REVERT: A  595 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8203 (mtmm)
  outliers start: 12
  outliers final: 11
  residues processed: 48
  average time/residue: 0.1393
  time to fit residues: 8.8503
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  : 0.444 
-------------------------------------------------------------------------------
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  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:    0.4980
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0970
   chunk 35 optimal weight:    0.4980
   chunk 36 optimal weight:    0.3980
   chunk 0 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0980
   chunk 14 optimal weight:    0.1980
   overall best weight:    0.2578

-------------------------------------------------------------------------------
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 = 0.3324 r_free = 0.3324 target = 0.107178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.093633 restraints weight = 6375.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.096427 restraints weight = 3766.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.098426 restraints weight = 2590.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3498

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= 0.168
  Angle     :  0.573   8.192   5464  Z= 0.289
  Chirality :  0.041   0.130    585
  Planarity :  0.004   0.048    718
  Dihedral  :  4.595  48.143    557
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.85 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.64 %
    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:  0.25 (0.37), residues: 491
  helix:  1.41 (0.42), residues: 138
  sheet:  0.93 (0.56), residues: 85
  loop : -0.76 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  57 
 HIS   0.004   0.001   HIS A 336 
 PHE   0.012   0.002   PHE A 139 
 TYR   0.015   0.002   TYR A 161 
 ARG   0.003   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03778 (  145)
  hydrogen bonds       : angle       4.91597 (  408)
  metal coordination   : bond        0.00433 (    2)
  covalent geometry    : bond        0.00401 ( 4019)
  covalent geometry    : angle       0.57257 ( 5464)
  Misc. bond           : bond        0.00062 (    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
  49 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A  440 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8098 (mtm180)
REVERT: A  459 MET cc_start: 0.8524 (mtt) cc_final: 0.8291 (mtt)
  outliers start: 13
  outliers final: 11
  residues processed: 49
  average time/residue: 0.1647
  time to fit residues: 10.2746
Evaluate side-chains
  45 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
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  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:    0.0980
   chunk 30 optimal weight:    0.1980
   chunk 29 optimal weight:    0.1980
   chunk 31 optimal weight:    0.8980
   chunk 38 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0470
   chunk 39 optimal weight:    0.0770
   chunk 40 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 46 optimal weight:    0.2980
   overall best weight:    0.1236

-------------------------------------------------------------------------------
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 = 0.3333 r_free = 0.3333 target = 0.107674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.094163 restraints weight = 6425.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.097048 restraints weight = 3734.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.098986 restraints weight = 2538.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3564

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= 0.112
  Angle     :  0.551   8.102   5464  Z= 0.275
  Chirality :  0.040   0.131    585
  Planarity :  0.004   0.049    718
  Dihedral  :  4.429  45.609    557
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.04 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 14.64 %
    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:  0.37 (0.37), residues: 491
  helix:  1.36 (0.42), residues: 144
  sheet:  1.04 (0.57), residues: 85
  loop : -0.66 (0.38), 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 336 
 PHE   0.008   0.001   PHE A  54 
 TYR   0.014   0.001   TYR A 161 
 ARG   0.006   0.000   ARG A 537 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03281 (  145)
  hydrogen bonds       : angle       4.81347 (  408)
  metal coordination   : bond        0.00184 (    2)
  covalent geometry    : bond        0.00270 ( 4019)
  covalent geometry    : angle       0.55137 ( 5464)
  Misc. bond           : bond        0.00031 (    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
  49 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 35
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A  191 TYR cc_start: 0.7677 (t80) cc_final: 0.7264 (t80)
REVERT: A  440 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8137 (mtm180)
REVERT: A  459 MET cc_start: 0.8474 (mtt) cc_final: 0.8204 (mtt)
REVERT: A  593 MET cc_start: 0.8063 (tpp) cc_final: 0.7834 (tpp)
REVERT: A  595 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8248 (mtmm)
  outliers start: 14
  outliers final: 11
  residues processed: 48
  average time/residue: 0.1498
  time to fit residues: 9.4118
Evaluate side-chains
  47 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 35
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    0.1980
   chunk 17 optimal weight:    0.0670
   chunk 45 optimal weight:    0.0980
   chunk 12 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0980
   chunk 34 optimal weight:    0.0970
   chunk 41 optimal weight:    0.1980
   chunk 29 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.1116

-------------------------------------------------------------------------------
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 = 0.3376 r_free = 0.3376 target = 0.110761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.097361 restraints weight = 6330.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.100259 restraints weight = 3683.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.102254 restraints weight = 2492.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4022  Z= 0.107
  Angle     :  0.541   7.724   5464  Z= 0.269
  Chirality :  0.040   0.136    585
  Planarity :  0.004   0.050    718
  Dihedral  :  4.258  40.921    557
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.65 %
    Favored  : 97.15 %
  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 (0.37), residues: 491
  helix:  1.40 (0.41), residues: 144
  sheet:  1.23 (0.58), residues: 85
  loop : -0.63 (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   0.008   0.001   PHE A  54 
 TYR   0.013   0.001   TYR A 161 
 ARG   0.005   0.000   ARG A 537 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03154 (  145)
  hydrogen bonds       : angle       4.76726 (  408)
  metal coordination   : bond        0.00191 (    2)
  covalent geometry    : bond        0.00258 ( 4019)
  covalent geometry    : angle       0.54114 ( 5464)
  Misc. bond           : bond        0.00027 (    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
  49 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A  106 MET cc_start: 0.8509 (tpt) cc_final: 0.7996 (tpt)
REVERT: A  440 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8193 (mtm180)
REVERT: A  459 MET cc_start: 0.8524 (mtt) cc_final: 0.8239 (mtt)
REVERT: A  593 MET cc_start: 0.8098 (tpp) cc_final: 0.7855 (tpp)
REVERT: A  595 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8267 (mtmm)
  outliers start: 13
  outliers final: 11
  residues processed: 49
  average time/residue: 0.1840
  time to fit residues: 11.6642
Evaluate side-chains
  48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0270
   chunk 4 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 33 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0970
   chunk 23 optimal weight:    0.4980
   chunk 47 optimal weight:    0.2980
   chunk 37 optimal weight:    0.1980
   chunk 5 optimal weight:    0.0970
   chunk 15 optimal weight:    0.3980
   overall best weight:    0.1434

-------------------------------------------------------------------------------
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 = 0.3354 r_free = 0.3354 target = 0.109172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.095909 restraints weight = 6294.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.098741 restraints weight = 3688.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.100679 restraints weight = 2519.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.3710

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= 0.116
  Angle     :  0.546   7.523   5464  Z= 0.271
  Chirality :  0.040   0.134    585
  Planarity :  0.004   0.050    718
  Dihedral  :  4.221  38.463    557
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.44 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.14 %
    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:  0.48 (0.37), residues: 491
  helix:  1.35 (0.41), residues: 144
  sheet:  1.27 (0.59), residues: 85
  loop : -0.60 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  57 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.008   0.001   PHE A  54 
 TYR   0.013   0.001   TYR A 161 
 ARG   0.006   0.000   ARG A 537 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03303 (  145)
  hydrogen bonds       : angle       4.78259 (  408)
  metal coordination   : bond        0.00237 (    2)
  covalent geometry    : bond        0.00280 ( 4019)
  covalent geometry    : angle       0.54627 ( 5464)
  Misc. bond           : bond        0.00033 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1876.92 seconds
wall clock time: 33 minutes 27.59 seconds (2007.59 seconds total)