Starting phenix.real_space_refine
on Tue Aug  4 14:15:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9z4i_73804/08_2026/9z4i_73804.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9z4i_73804/08_2026/9z4i_73804.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9z4i_73804/08_2026/9z4i_73804.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9z4i_73804/08_2026/9z4i_73804.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9z4i_73804/08_2026/9z4i_73804.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9z4i_73804/08_2026/9z4i_73804.cif"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.004
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
     S      18      5.16       5
     Na      1      4.78       5
     C    2501      2.51       5
     N     594      2.21       5
     O     634      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3748
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 487, 3747
          Classifications: {'peptide': 487}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 21, 'TRANS': 465}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.69, per 1000 atoms: 0.18
  Number of scatterers: 3748
  At special positions: 0
  Unit cell: (72.814, 89.16, 90.646, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     Na      1     11.00
     O     634      8.00
     N     594      7.00
     C    2501      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  65 " - pdb=" SG  CYS A  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 136.1 milliseconds
  

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  900

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      77.2% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 63 through 71
      removed outlier: 3.509A  pdb=" N   PHE A  67 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 90
    Processing helix  chain 'A' and resid 92 through 94
      No H-bonds generated for 'chain 'A' and resid 92 through 94'
    Processing helix  chain 'A' and resid 95 through 121
      removed outlier: 3.504A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 134
    Processing helix  chain 'A' and resid 136 through 162
      removed outlier: 4.422A  pdb=" N   LEU A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ALA A 146 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      Proline residue:  A 152  - end of helix
    Processing helix  chain 'A' and resid 166 through 193
      removed outlier: 4.166A  pdb=" N   ALA A 170 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE A 171 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLY A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   VAL A 185 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ALA A 186 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 223
    Processing helix  chain 'A' and resid 227 through 249
      removed outlier: 3.703A  pdb=" N   LEU A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 310
      removed outlier: 3.632A  pdb=" N   GLN A 307 " --> pdb=" O   GLN A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 342
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 358 through 374
      removed outlier: 4.362A  pdb=" N   VAL A 364 " --> pdb=" O   CYS A 360 " (cutoff:3.500A)
      Proline residue:  A 367  - end of helix
    Processing helix  chain 'A' and resid 389 through 408
      removed outlier: 4.296A  pdb=" N   ALA A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 452
      removed outlier: 3.739A  pdb=" N   ALA A 422 " --> pdb=" O   HIS A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 482
      removed outlier: 3.875A  pdb=" N   LEU A 463 " --> pdb=" O   GLY A 459 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   ALA A 464 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   GLY A 470 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ASP A 471 " --> pdb=" O   ASN A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 515
      removed outlier: 3.782A  pdb=" N   PHE A 492 " --> pdb=" O   PHE A 488 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   VAL A 503 " --> pdb=" O   ILE A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 549
      Proline residue:  A 547  - end of helix
    Processing helix  chain 'A' and resid 554 through 578
      removed outlier: 3.692A  pdb=" N   GLY A 558 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 226
      removed outlier: 3.510A  pdb=" N   ILE A 225 " --> pdb=" O   VAL A 519 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL A 519 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1

    268 hydrogen bonds defined for protein.
    798 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: 0.52

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1129
        1.34 -     1.46: 947
        1.46 -     1.58: 1745
        1.58 -     1.69: 0
        1.69 -     1.81: 22
  Bond restraints: 3843
  Sorted by residual:
  bond pdb=" N   GLN A 549 "
       pdb=" CA  GLN A 549 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.40e-02 5.10e+03 3.96e+00
  bond pdb=" N   ALA A  49 "
       pdb=" CA  ALA A  49 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.81e+00
  bond pdb=" CA  VAL A 546 "
       pdb=" CB  VAL A 546 "
    ideal  model  delta    sigma   weight residual
    1.539  1.535  0.004 5.40e-03 3.43e+04 4.37e-01
  bond pdb=" N   ILE A 384 "
       pdb=" CA  ILE A 384 "
    ideal  model  delta    sigma   weight residual
    1.465  1.473 -0.008 1.38e-02 5.25e+03 3.59e-01
  bond pdb=" C   GLN A 549 "
       pdb=" N   CYS A 550 "
    ideal  model  delta    sigma   weight residual
    1.333  1.340 -0.007 1.39e-02 5.18e+03 2.89e-01
  ... (remaining 3838 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 5047
        0.98 -     1.96: 165
        1.96 -     2.93: 18
        2.93 -     3.91: 19
        3.91 -     4.89: 7
  Bond angle restraints: 5256
  Sorted by residual:
  angle pdb=" N   GLN A 549 "
        pdb=" CA  GLN A 549 "
        pdb=" C   GLN A 549 "
      ideal   model   delta    sigma   weight residual
     113.15  110.31    2.84 1.19e+00 7.06e-01 5.69e+00
  angle pdb=" N   ARG A 356 "
        pdb=" CA  ARG A 356 "
        pdb=" C   ARG A 356 "
      ideal   model   delta    sigma   weight residual
     109.81  114.70   -4.89 2.21e+00 2.05e-01 4.90e+00
  angle pdb=" CA  GLN A 549 "
        pdb=" C   GLN A 549 "
        pdb=" O   GLN A 549 "
      ideal   model   delta    sigma   weight residual
     119.23  115.99    3.24 1.54e+00 4.22e-01 4.42e+00
  angle pdb=" C   GLN A 549 "
        pdb=" CA  GLN A 549 "
        pdb=" CB  GLN A 549 "
      ideal   model   delta    sigma   weight residual
     110.36  106.56    3.80 1.85e+00 2.92e-01 4.22e+00
  angle pdb=" C   VAL A 142 "
        pdb=" N   THR A 143 "
        pdb=" CA  THR A 143 "
      ideal   model   delta    sigma   weight residual
     122.42  119.89    2.53 1.55e+00 4.16e-01 2.67e+00
  ... (remaining 5251 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.49: 2014
       12.49 -    24.98: 148
       24.98 -    37.47: 37
       37.47 -    49.96: 10
       49.96 -    62.45: 2
  Dihedral angle restraints: 2211
    sinusoidal: 809
      harmonic: 1402
  Sorted by residual:
  dihedral pdb=" CA  ARG A 356 "
           pdb=" C   ARG A 356 "
           pdb=" N   PRO A 357 "
           pdb=" CA  PRO A 357 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.30  -29.70     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CB  CYS A  65 "
           pdb=" SG  CYS A  65 "
           pdb=" SG  CYS A  89 "
           pdb=" CB  CYS A  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.64   39.64     1      1.00e+01 1.00e-02 2.21e+01
  dihedral pdb=" CA  THR A 143 "
           pdb=" C   THR A 143 "
           pdb=" N   PHE A 144 "
           pdb=" CA  PHE A 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.18  -15.82     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 2208 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 502
       0.042 -    0.083: 119
       0.083 -    0.125: 18
       0.125 -    0.166: 2
       0.166 -    0.208: 1
  Chirality restraints: 642
  Sorted by residual:
  chirality pdb=" CA  GLN A 549 "
            pdb=" N   GLN A 549 "
            pdb=" C   GLN A 549 "
            pdb=" CB  GLN A 549 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  PRO A 357 "
            pdb=" N   PRO A 357 "
            pdb=" C   PRO A 357 "
            pdb=" CB  PRO A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.14e-01
  chirality pdb=" CA  VAL A 519 "
            pdb=" N   VAL A 519 "
            pdb=" C   VAL A 519 "
            pdb=" CB  VAL A 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.97e-01
  ... (remaining 639 not shown)

  Planarity restraints: 638
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 461 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.03e+00
        pdb=" C   THR A 461 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   THR A 461 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A 462 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 143 "    0.006 2.00e-02 2.50e+03   1.19e-02 1.41e+00
        pdb=" C   THR A 143 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   THR A 143 "    0.008 2.00e-02 2.50e+03
        pdb=" N   PHE A 144 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 310 "   -0.016 5.00e-02 4.00e+02   2.49e-02 9.94e-01
        pdb=" N   PRO A 311 "    0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO A 311 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 311 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 635 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 877
        2.79 -     3.32: 3939
        3.32 -     3.84: 6046
        3.84 -     4.37: 6510
        4.37 -     4.90: 11952
  Nonbonded interactions: 29324
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 145 "
            pdb=" ND2 ASN A 149 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" OD1 ASP A  52 "
            pdb=" N   CYS A  53 "
     model   vdw
     2.356 3.120
  nonbonded pdb=" OD1 ASP A 350 "
            pdb=" N   ASP A 351 "
     model   vdw
     2.415 3.120
  nonbonded pdb=" OD2 ASP A 313 "
            pdb=" N   ARG A 315 "
     model   vdw
     2.472 3.120
  nonbonded pdb=" O   VAL A 159 "
            pdb=" OG  SER A 162 "
     model   vdw
     2.472 3.040
  ... (remaining 29319 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.510
  Find NCS groups from input model:        0.010
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
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      :  0.003   0.032   3845  Z= 0.123
  Angle     :  0.477   4.890   5260  Z= 0.263
  Chirality :  0.036   0.208    642
  Planarity :  0.003   0.025    638
  Dihedral  : 10.102  62.448   1305
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  4.94 %
    Favored  : 94.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.39), residues: 483
  helix:  1.90 (0.28), residues: 359
  sheet:  None (None), residues: 0
  loop : -1.47 (0.53), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 204 
 TYR   0.007   0.001   TYR A 233 
 PHE   0.004   0.001   PHE A 122 
 TRP   0.006   0.001   TRP A 529 
 HIS   0.002   0.001   HIS A 515 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 ( 3843)
  covalent geometry    : angle       0.47714 /  0.26 ( 5256)
  SS BOND              : bond        0.00096 /  0.05 (    2)
  SS BOND              : angle       0.78062 /  0.45 (    4)
  hydrogen bonds       : bond        0.09043 /  5.34 (  268)
  hydrogen bonds       : angle       4.54592 /  3.24 (  798)

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

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

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8119 (pt) cc_final: 0.7867 (pt)
  outliers start: 1
  outliers final: 1
  residues processed: 75
  average time/residue: 0.0606
  time to fit residues: 5.8243
Evaluate side-chains
  65 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  527 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0170
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.2980
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.6220

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  60 ASN
A 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.181743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.155895 restraints weight = 4900.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.159880 restraints weight = 2853.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.162327 restraints weight = 2026.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.164221 restraints weight = 1625.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.165261 restraints weight = 1384.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3845  Z= 0.120
  Angle     :  0.555   7.279   5260  Z= 0.273
  Chirality :  0.039   0.134    642
  Planarity :  0.004   0.028    638
  Dihedral  :  4.451  47.457    521
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.63 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.39), residues: 483
  helix:  2.06 (0.27), residues: 352
  sheet:  None (None), residues: 0
  loop : -1.28 (0.54), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 315 
 TYR   0.010   0.001   TYR A 233 
 PHE   0.010   0.001   PHE A 122 
 TRP   0.019   0.001   TRP A 354 
 HIS   0.003   0.001   HIS A 418 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 3843)
  covalent geometry    : angle       0.55455 /  0.27 ( 5256)
  SS BOND              : bond        0.00088 /  0.04 (    2)
  SS BOND              : angle       0.97558 /  0.58 (    4)
  hydrogen bonds       : bond        0.03911 /  2.53 (  268)
  hydrogen bonds       : angle       3.95030 /  2.86 (  798)

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

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

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.7969 (pt) cc_final: 0.7683 (pt)
REVERT: A  349 LYS cc_start: 0.8267 (mmmm) cc_final: 0.7955 (mmmt)
  outliers start: 7
  outliers final: 6
  residues processed: 68
  average time/residue: 0.0374
  time to fit residues: 3.3160
Evaluate side-chains
  64 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  391 TRP
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  572 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 320 GLN
A 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.177027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.151518 restraints weight = 4743.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.155338 restraints weight = 2770.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.157835 restraints weight = 1975.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.159480 restraints weight = 1582.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.160467 restraints weight = 1362.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3845  Z= 0.122
  Angle     :  0.530   6.711   5260  Z= 0.263
  Chirality :  0.038   0.154    642
  Planarity :  0.004   0.033    638
  Dihedral  :  4.396  47.389    521
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 11.11 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.39), residues: 483
  helix:  2.04 (0.28), residues: 359
  sheet:  None (None), residues: 0
  loop : -1.64 (0.53), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 315 
 TYR   0.008   0.001   TYR A 565 
 PHE   0.014   0.001   PHE A 406 
 TRP   0.021   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A 418 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 3843)
  covalent geometry    : angle       0.52946 /  0.26 ( 5256)
  SS BOND              : bond        0.00101 /  0.05 (    2)
  SS BOND              : angle       0.85877 /  0.50 (    4)
  hydrogen bonds       : bond        0.03945 /  2.56 (  268)
  hydrogen bonds       : angle       3.91446 /  2.83 (  798)

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

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

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A  349 LYS cc_start: 0.8260 (mmmm) cc_final: 0.7959 (mmtm)
  outliers start: 8
  outliers final: 7
  residues processed: 65
  average time/residue: 0.0401
  time to fit residues: 3.3706
Evaluate side-chains
  65 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  391 TRP
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  572 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.7980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.179662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.153265 restraints weight = 4859.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.157226 restraints weight = 2878.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.159565 restraints weight = 2064.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.161306 restraints weight = 1673.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.161829 restraints weight = 1447.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3845  Z= 0.121
  Angle     :  0.520   7.132   5260  Z= 0.260
  Chirality :  0.038   0.133    642
  Planarity :  0.004   0.033    638
  Dihedral  :  4.363  47.652    521
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.35 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.40), residues: 483
  helix:  2.04 (0.28), residues: 359
  sheet:  None (None), residues: 0
  loop : -1.31 (0.57), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  64 
 TYR   0.008   0.001   TYR A 565 
 PHE   0.008   0.001   PHE A 122 
 TRP   0.018   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A 418 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 3843)
  covalent geometry    : angle       0.51925 /  0.26 ( 5256)
  SS BOND              : bond        0.00070 /  0.03 (    2)
  SS BOND              : angle       0.78463 /  0.47 (    4)
  hydrogen bonds       : bond        0.03892 /  2.53 (  268)
  hydrogen bonds       : angle       3.86846 /  2.79 (  798)

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

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

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  306 LEU cc_start: 0.8333 (tp) cc_final: 0.7796 (mp)
REVERT: A  349 LYS cc_start: 0.8236 (mmmm) cc_final: 0.7908 (mmtm)
  outliers start: 8
  outliers final: 8
  residues processed: 65
  average time/residue: 0.0482
  time to fit residues: 4.1437
Evaluate side-chains
  67 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  391 TRP
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  572 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.0982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.176155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.149936 restraints weight = 4837.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.153642 restraints weight = 2881.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.156013 restraints weight = 2082.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.157462 restraints weight = 1697.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.158551 restraints weight = 1486.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3845  Z= 0.141
  Angle     :  0.525   6.972   5260  Z= 0.267
  Chirality :  0.038   0.132    642
  Planarity :  0.004   0.034    638
  Dihedral  :  4.416  47.274    521
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.09 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.40), residues: 483
  helix:  2.01 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.38 (0.56), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  54 
 TYR   0.008   0.001   TYR A 565 
 PHE   0.015   0.001   PHE A 406 
 TRP   0.013   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A 418 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.14 ( 3843)
  covalent geometry    : angle       0.52475 /  0.27 ( 5256)
  SS BOND              : bond        0.00118 /  0.06 (    2)
  SS BOND              : angle       0.90352 /  0.53 (    4)
  hydrogen bonds       : bond        0.04161 /  2.71 (  268)
  hydrogen bonds       : angle       3.89725 /  2.81 (  798)

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

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

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  306 LEU cc_start: 0.8311 (tp) cc_final: 0.7775 (mp)
REVERT: A  349 LYS cc_start: 0.8273 (mmmm) cc_final: 0.7952 (mmtm)
  outliers start: 11
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0577
  time to fit residues: 4.9360
Evaluate side-chains
  69 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  391 TRP
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  572 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 25 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.7580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.178402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.151624 restraints weight = 4878.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.155417 restraints weight = 2852.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.157970 restraints weight = 2045.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.159479 restraints weight = 1649.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.160548 restraints weight = 1437.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3845  Z= 0.117
  Angle     :  0.500   6.678   5260  Z= 0.255
  Chirality :  0.038   0.131    642
  Planarity :  0.004   0.034    638
  Dihedral  :  4.377  47.888    521
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.33 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.40), residues: 483
  helix:  2.11 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.42 (0.56), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 485 
 TYR   0.008   0.001   TYR A 565 
 PHE   0.007   0.001   PHE A 122 
 TRP   0.012   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A 418 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 3843)
  covalent geometry    : angle       0.50022 /  0.25 ( 5256)
  SS BOND              : bond        0.00096 /  0.05 (    2)
  SS BOND              : angle       0.78587 /  0.46 (    4)
  hydrogen bonds       : bond        0.03887 /  2.53 (  268)
  hydrogen bonds       : angle       3.85438 /  2.78 (  798)

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

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

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  149 ASN cc_start: 0.7146 (m-40) cc_final: 0.6886 (m-40)
REVERT: A  349 LYS cc_start: 0.8269 (mmmm) cc_final: 0.7947 (mmtm)
  outliers start: 11
  outliers final: 10
  residues processed: 66
  average time/residue: 0.0593
  time to fit residues: 5.0832
Evaluate side-chains
  69 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 ASN
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  391 TRP
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  572 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 31 optimal weight:    0.2980
   chunk 28 optimal weight:    0.0370
   chunk 38 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0970
   chunk 25 optimal weight:    0.0370
   overall best weight:    0.2134

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.183350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.157256 restraints weight = 4904.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.160981 restraints weight = 2886.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.163515 restraints weight = 2076.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.165009 restraints weight = 1667.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.166212 restraints weight = 1449.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3845  Z= 0.097
  Angle     :  0.470   6.173   5260  Z= 0.238
  Chirality :  0.037   0.121    642
  Planarity :  0.004   0.032    638
  Dihedral  :  4.274  49.224    521
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.57 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.40), residues: 483
  helix:  2.25 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -1.37 (0.57), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 480 
 TYR   0.008   0.001   TYR A 565 
 PHE   0.018   0.001   PHE A 406 
 TRP   0.013   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A 418 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00191 /  0.10 ( 3843)
  covalent geometry    : angle       0.47019 /  0.24 ( 5256)
  SS BOND              : bond        0.00030 /  0.01 (    2)
  SS BOND              : angle       0.39070 /  0.23 (    4)
  hydrogen bonds       : bond        0.03308 /  2.16 (  268)
  hydrogen bonds       : angle       3.77121 /  2.72 (  798)

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

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

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A   70 ARG cc_start: 0.7508 (ttt-90) cc_final: 0.7180 (ttp80)
REVERT: A  149 ASN cc_start: 0.7125 (m-40) cc_final: 0.6835 (m-40)
REVERT: A  349 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7942 (mmtm)
  outliers start: 11
  outliers final: 8
  residues processed: 69
  average time/residue: 0.0566
  time to fit residues: 5.0890
Evaluate side-chains
  66 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  317 TRP
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  391 TRP
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  573 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 34 optimal weight:    0.3980
   chunk 1 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.6380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.179986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.153642 restraints weight = 4868.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.157367 restraints weight = 2856.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.159914 restraints weight = 2053.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.161431 restraints weight = 1653.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.162509 restraints weight = 1437.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3845  Z= 0.110
  Angle     :  0.495   7.266   5260  Z= 0.251
  Chirality :  0.038   0.122    642
  Planarity :  0.004   0.032    638
  Dihedral  :  4.249  47.883    521
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.31 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.40), residues: 483
  helix:  2.19 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -1.36 (0.56), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 416 
 TYR   0.008   0.001   TYR A 565 
 PHE   0.006   0.001   PHE A 122 
 TRP   0.012   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A 418 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 ( 3843)
  covalent geometry    : angle       0.49531 /  0.25 ( 5256)
  SS BOND              : bond        0.00073 /  0.04 (    2)
  SS BOND              : angle       0.60117 /  0.36 (    4)
  hydrogen bonds       : bond        0.03618 /  2.37 (  268)
  hydrogen bonds       : angle       3.80986 /  2.74 (  798)

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

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

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  149 ASN cc_start: 0.7106 (m-40) cc_final: 0.6843 (m-40)
REVERT: A  349 LYS cc_start: 0.8217 (mmmm) cc_final: 0.8003 (mmtm)
  outliers start: 9
  outliers final: 7
  residues processed: 67
  average time/residue: 0.0577
  time to fit residues: 5.0399
Evaluate side-chains
  67 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 ASN
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  317 TRP
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  391 TRP
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  572 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 45 optimal weight:    0.0570
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0050
   chunk 43 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 0 optimal weight:    0.6980
   overall best weight:    0.4712

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.181571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.155485 restraints weight = 4836.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.159208 restraints weight = 2863.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.161569 restraints weight = 2068.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.163286 restraints weight = 1676.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.164354 restraints weight = 1452.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3845  Z= 0.101
  Angle     :  0.486   6.981   5260  Z= 0.246
  Chirality :  0.037   0.123    642
  Planarity :  0.004   0.032    638
  Dihedral  :  4.229  48.021    521
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 16.05 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.40), residues: 483
  helix:  2.21 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -1.34 (0.57), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A  64 
 TYR   0.008   0.001   TYR A 565 
 PHE   0.023   0.001   PHE A 406 
 TRP   0.011   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A 418 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.10 ( 3843)
  covalent geometry    : angle       0.48622 /  0.25 ( 5256)
  SS BOND              : bond        0.00033 /  0.02 (    2)
  SS BOND              : angle       0.55823 /  0.34 (    4)
  hydrogen bonds       : bond        0.03487 /  2.28 (  268)
  hydrogen bonds       : angle       3.79567 /  2.72 (  798)

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

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

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  149 ASN cc_start: 0.7112 (m-40) cc_final: 0.6842 (m-40)
  outliers start: 7
  outliers final: 7
  residues processed: 65
  average time/residue: 0.0552
  time to fit residues: 4.6824
Evaluate side-chains
  66 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 ASN
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  317 TRP
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  391 TRP
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  572 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 21 optimal weight:    0.0670
   chunk 28 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 38 optimal weight:    0.3980
   chunk 22 optimal weight:    0.0870
   overall best weight:    0.3896

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.182138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.155927 restraints weight = 4914.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.159526 restraints weight = 2891.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.162159 restraints weight = 2085.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.163769 restraints weight = 1677.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.164922 restraints weight = 1450.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3845  Z= 0.100
  Angle     :  0.483   6.821   5260  Z= 0.244
  Chirality :  0.037   0.122    642
  Planarity :  0.003   0.032    638
  Dihedral  :  4.200  47.786    521
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 16.54 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.40), residues: 483
  helix:  2.19 (0.28), residues: 362
  sheet:  None (None), residues: 0
  loop : -1.25 (0.58), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  64 
 TYR   0.008   0.001   TYR A 565 
 PHE   0.007   0.001   PHE A 217 
 TRP   0.011   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00208 /  0.10 ( 3843)
  covalent geometry    : angle       0.48281 /  0.24 ( 5256)
  SS BOND              : bond        0.00043 /  0.02 (    2)
  SS BOND              : angle       0.56258 /  0.34 (    4)
  hydrogen bonds       : bond        0.03436 /  2.25 (  268)
  hydrogen bonds       : angle       3.78920 /  2.72 (  798)

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

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

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  966 Ramachandran restraints generated.
    483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  149 ASN cc_start: 0.7178 (m-40) cc_final: 0.6906 (m-40)
  outliers start: 7
  outliers final: 7
  residues processed: 63
  average time/residue: 0.0505
  time to fit residues: 4.1646
Evaluate side-chains
  65 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 ASN
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  317 TRP
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  391 TRP
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  572 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0980
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0170
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.4420

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.182789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.156330 restraints weight = 4723.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.160050 restraints weight = 2827.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.162482 restraints weight = 2046.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.163972 restraints weight = 1664.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.164946 restraints weight = 1454.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3845  Z= 0.101
  Angle     :  0.483   6.961   5260  Z= 0.245
  Chirality :  0.037   0.123    642
  Planarity :  0.004   0.032    638
  Dihedral  :  4.185  47.380    521
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.05 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.40), residues: 483
  helix:  2.16 (0.28), residues: 362
  sheet:  None (None), residues: 0
  loop : -1.23 (0.58), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 416 
 TYR   0.008   0.001   TYR A 565 
 PHE   0.024   0.001   PHE A 406 
 TRP   0.016   0.001   TRP A 465 
 HIS   0.002   0.001   HIS A  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00213 /  0.10 ( 3843)
  covalent geometry    : angle       0.48305 /  0.24 ( 5256)
  SS BOND              : bond        0.00045 /  0.02 (    2)
  SS BOND              : angle       0.56765 /  0.34 (    4)
  hydrogen bonds       : bond        0.03459 /  2.26 (  268)
  hydrogen bonds       : angle       3.79385 /  2.72 (  798)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 790.59 seconds
wall clock time: 14 minutes 12.68 seconds (852.68 seconds total)