Starting phenix.real_space_refine
on Tue Mar  3 12:41:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qzo_53472/03_2026/9qzo_53472.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qzo_53472/03_2026/9qzo_53472.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qzo_53472/03_2026/9qzo_53472.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qzo_53472/03_2026/9qzo_53472.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qzo_53472/03_2026/9qzo_53472.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qzo_53472/03_2026/9qzo_53472.cif"
  }
  resolution = 2.9
  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=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    2802      2.51       5
     N     687      2.21       5
     O     742      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4266
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 550, 4231
          Classifications: {'peptide': 550}
          Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 517}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.86, per 1000 atoms: 0.20
  Number of scatterers: 4266
  At special positions: 0
  Unit cell: (85.644, 97.356, 74.664, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O     742      8.00
     N     687      7.00
     C    2802      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 419 " - pdb=" SG  CYS A 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 444 " - pdb=" SG  CYS A 494 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 450 " - pdb=" SG  CYS A 470 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 492 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 580 " - pdb=" SG  CYS A 594 " 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: 0.31
  Conformation dependent library (CDL) restraints added in 291.0 milliseconds
  

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1020

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 2 sheets defined
      70.2% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 64
      removed outlier: 3.817A  pdb=" N   PHE A  34 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   THR A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   THR A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 91
      removed outlier: 4.109A  pdb=" N   ASN A  77 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   GLU A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   ILE A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   PHE A  87 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   PHE A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
    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 96 through 122
      Proline residue:  A 118  - end of helix
    Processing helix  chain 'A' and resid 168 through 184
    Processing helix  chain 'A' and resid 186 through 199
    Processing helix  chain 'A' and resid 203 through 215
    Processing helix  chain 'A' and resid 217 through 230
    Processing helix  chain 'A' and resid 256 through 273
      removed outlier: 3.608A  pdb=" N   GLY A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 277
    Processing helix  chain 'A' and resid 306 through 323
      Proline residue:  A 315  - end of helix
    Processing helix  chain 'A' and resid 324 through 357
      removed outlier: 3.758A  pdb=" N   VAL A 340 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR A 346 " --> pdb=" O   ALA A 342 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   ASN A 349 " --> pdb=" O   SER A 345 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   LYS A 350 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 389
      removed outlier: 4.411A  pdb=" N   LEU A 372 " --> pdb=" O   GLY A 368 " (cutoff:3.500A)
      Proline residue:  A 373  - end of helix
    Processing helix  chain 'A' and resid 394 through 411
      removed outlier: 4.300A  pdb=" N   ARG A 398 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 416
    Processing helix  chain 'A' and resid 442 through 446
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'
    Processing helix  chain 'A' and resid 514 through 531
      removed outlier: 3.576A  pdb=" N   ILE A 531 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 543
    Processing helix  chain 'A' and resid 545 through 547
      No H-bonds generated for 'chain 'A' and resid 545 through 547'
    Processing helix  chain 'A' and resid 548 through 564
    Processing helix  chain 'A' and resid 566 through 578
      removed outlier: 4.383A  pdb=" N   SER A 570 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 635
      removed outlier: 3.745A  pdb=" N   GLN A 610 " --> pdb=" O   TYR A 606 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 466
      removed outlier: 3.709A  pdb=" N   ILE A 488 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 585
      removed outlier: 5.091A  pdb=" N   CYS A 580 " --> pdb=" O   TYR A 596 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   TYR A 596 " --> pdb=" O   CYS A 580 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   ARG A 582 " --> pdb=" O   CYS A 594 " (cutoff:3.500A)
      removed outlier: 5.322A  pdb=" N   CYS A 594 " --> pdb=" O   ARG A 582 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   ASN A 584 " --> pdb=" O   GLY A 592 " (cutoff:3.500A)

    282 hydrogen bonds defined for protein.
    822 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: 0.86

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 635
        1.32 -     1.44: 1233
        1.44 -     1.57: 2461
        1.57 -     1.69: 0
        1.69 -     1.82: 51
  Bond restraints: 4380
  Sorted by residual:
  bond pdb=" CB  GLN A 126 "
       pdb=" CG  GLN A 126 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.29e+00
  bond pdb=" CAL Y01 A 701 "
       pdb=" CAX Y01 A 701 "
    ideal  model  delta    sigma   weight residual
    1.540  1.518  0.022 2.00e-02 2.50e+03 1.19e+00
  bond pdb=" CAJ Y01 A 701 "
       pdb=" CAN Y01 A 701 "
    ideal  model  delta    sigma   weight residual
    1.524  1.502  0.022 2.00e-02 2.50e+03 1.18e+00
  bond pdb=" CG  GLN A 126 "
       pdb=" CD  GLN A 126 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.01e-01
  bond pdb=" CBC Y01 A 701 "
       pdb=" OAW Y01 A 701 "
    ideal  model  delta    sigma   weight residual
    1.437  1.456 -0.019 2.00e-02 2.50e+03 8.75e-01
  ... (remaining 4375 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 5846
        1.57 -     3.15: 88
        3.15 -     4.72: 14
        4.72 -     6.29: 10
        6.29 -     7.87: 1
  Bond angle restraints: 5959
  Sorted by residual:
  angle pdb=" C   CYS A 507 "
        pdb=" CA  CYS A 507 "
        pdb=" CB  CYS A 507 "
      ideal   model   delta    sigma   weight residual
     108.61  112.67   -4.06 1.53e+00 4.27e-01 7.03e+00
  angle pdb=" CB  GLN A 126 "
        pdb=" CG  GLN A 126 "
        pdb=" CD  GLN A 126 "
      ideal   model   delta    sigma   weight residual
     112.60  117.03   -4.43 1.70e+00 3.46e-01 6.79e+00
  angle pdb=" CA  LEU A 307 "
        pdb=" CB  LEU A 307 "
        pdb=" CG  LEU A 307 "
      ideal   model   delta    sigma   weight residual
     116.30  124.17   -7.87 3.50e+00 8.16e-02 5.05e+00
  angle pdb=" CB  MET A 539 "
        pdb=" CG  MET A 539 "
        pdb=" SD  MET A 539 "
      ideal   model   delta    sigma   weight residual
     112.70  106.56    6.14 3.00e+00 1.11e-01 4.19e+00
  angle pdb=" C   VAL A 390 "
        pdb=" CA  VAL A 390 "
        pdb=" CB  VAL A 390 "
      ideal   model   delta    sigma   weight residual
     111.23  113.32   -2.09 1.08e+00 8.57e-01 3.73e+00
  ... (remaining 5954 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 2383
       17.64 -    35.28: 198
       35.28 -    52.92: 54
       52.92 -    70.56: 6
       70.56 -    88.20: 4
  Dihedral angle restraints: 2645
    sinusoidal: 1056
      harmonic: 1589
  Sorted by residual:
  dihedral pdb=" CB  CYS A 459 "
           pdb=" SG  CYS A 459 "
           pdb=" SG  CYS A 507 "
           pdb=" CB  CYS A 507 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.80  -88.20     1      1.00e+01 1.00e-02 9.30e+01
  dihedral pdb=" CB  CYS A 450 "
           pdb=" SG  CYS A 450 "
           pdb=" SG  CYS A 470 "
           pdb=" CB  CYS A 470 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -35.45  -50.55     1      1.00e+01 1.00e-02 3.50e+01
  dihedral pdb=" CA  CYS A 507 "
           pdb=" C   CYS A 507 "
           pdb=" N   PRO A 508 "
           pdb=" CA  PRO A 508 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.89  -20.11     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 2642 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 394
       0.024 -    0.049: 157
       0.049 -    0.073: 78
       0.073 -    0.097: 40
       0.097 -    0.121: 17
  Chirality restraints: 686
  Sorted by residual:
  chirality pdb=" CA  ILE A 232 "
            pdb=" N   ILE A 232 "
            pdb=" C   ILE A 232 "
            pdb=" CB  ILE A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.68e-01
  chirality pdb=" CA  VAL A 424 "
            pdb=" N   VAL A 424 "
            pdb=" C   VAL A 424 "
            pdb=" CB  VAL A 424 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.46e-01
  chirality pdb=" CA  THR A 346 "
            pdb=" N   THR A 346 "
            pdb=" C   THR A 346 "
            pdb=" CB  THR A 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.41    0.12 2.00e-01 2.50e+01 3.42e-01
  ... (remaining 683 not shown)

  Planarity restraints: 737
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 117 "    0.027 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO A 118 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 118 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 118 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 247 "   -0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO A 248 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 248 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 248 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 390 "   -0.006 2.00e-02 2.50e+03   1.26e-02 1.60e+00
        pdb=" C   VAL A 390 "    0.022 2.00e-02 2.50e+03
        pdb=" O   VAL A 390 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   PHE A 391 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 734 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1178
        2.81 -     3.34: 4247
        3.34 -     3.86: 7093
        3.86 -     4.38: 8125
        4.38 -     4.90: 14263
  Nonbonded interactions: 34906
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 468 "
            pdb=" ND1 HIS A 471 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   ILE A  79 "
            pdb=" OG1 THR A  83 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ILE A  85 "
            pdb=" OG  SER A  89 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   ARG A  94 "
            pdb=" NH2 ARG A 280 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" OE2 GLU A 465 "
            pdb=" OH  TYR A 596 "
     model   vdw
     2.344 3.040
  ... (remaining 34901 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.770
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:             0.010
  Load rotamer database and sin/cos tables:6.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
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   0.034   4386  Z= 0.126
  Angle     :  0.538   7.867   5971  Z= 0.272
  Chirality :  0.039   0.121    686
  Planarity :  0.004   0.040    737
  Dihedral  : 14.247  86.749   1607
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 14.35 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.00 (0.37), residues: 544
  helix:  2.67 (0.28), residues: 354
  sheet:  None (None), residues: 0
  loop :  0.76 (0.48), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 445 
 TYR   0.007   0.001   TYR A 194 
 PHE   0.014   0.001   PHE A 310 
 TRP   0.004   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4380)
  covalent geometry    : angle       0.53761 ( 5959)
  SS BOND              : bond        0.00177 (    6)
  SS BOND              : angle       0.77216 (   12)
  hydrogen bonds       : bond        0.12999 (  282)
  hydrogen bonds       : angle       5.24390 (  822)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 4
  residues processed: 65
  average time/residue: 0.6670
  time to fit residues: 44.6787
Evaluate side-chains
  46 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  540 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 349 ASN
A 355 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.077565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.058692 restraints weight = 10568.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 3.14
r_work: 0.2733 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4386  Z= 0.158
  Angle     :  0.589   8.491   5971  Z= 0.283
  Chirality :  0.042   0.212    686
  Planarity :  0.004   0.039    737
  Dihedral  :  6.026  57.449    669
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.63 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  2.93 (0.37), residues: 544
  helix:  2.67 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop :  0.55 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 446 
 TYR   0.009   0.001   TYR A 489 
 PHE   0.012   0.001   PHE A 198 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 4380)
  covalent geometry    : angle       0.58855 ( 5959)
  SS BOND              : bond        0.00181 (    6)
  SS BOND              : angle       0.87998 (   12)
  hydrogen bonds       : bond        0.04362 (  282)
  hydrogen bonds       : angle       4.25368 (  822)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  353 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8326 (mt-10)
REVERT: A  510 SER cc_start: 0.9081 (m) cc_final: 0.8840 (t)
  outliers start: 14
  outliers final: 5
  residues processed: 54
  average time/residue: 0.5304
  time to fit residues: 29.7119
Evaluate side-chains
  45 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  548 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 41 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0060
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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 = 0.3323 r_free = 0.3323 target = 0.078249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.059134 restraints weight = 10659.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 3.15
r_work: 0.2761 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4386  Z= 0.118
  Angle     :  0.553   7.584   5971  Z= 0.267
  Chirality :  0.042   0.222    686
  Planarity :  0.004   0.038    737
  Dihedral  :  5.830  56.281    664
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.20 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.01 (0.37), residues: 544
  helix:  2.76 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop :  0.47 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 446 
 TYR   0.006   0.001   TYR A 194 
 PHE   0.020   0.001   PHE A 337 
 TRP   0.003   0.001   TRP A 626 
 HIS   0.002   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4380)
  covalent geometry    : angle       0.55058 ( 5959)
  SS BOND              : bond        0.00090 (    6)
  SS BOND              : angle       1.32113 (   12)
  hydrogen bonds       : bond        0.03703 (  282)
  hydrogen bonds       : angle       4.03854 (  822)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  196 ASP cc_start: 0.8930 (t70) cc_final: 0.8410 (t70)
REVERT: A  200 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7360 (tm-30)
REVERT: A  353 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8330 (mt-10)
REVERT: A  386 MET cc_start: 0.9242 (mmt) cc_final: 0.8863 (tpp)
  outliers start: 15
  outliers final: 2
  residues processed: 47
  average time/residue: 0.6000
  time to fit residues: 29.2292
Evaluate side-chains
  41 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  170 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    0.4980
   chunk 37 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3300 r_free = 0.3300 target = 0.076876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.057698 restraints weight = 10708.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 3.11
r_work: 0.2719 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4386  Z= 0.146
  Angle     :  0.546   6.578   5971  Z= 0.264
  Chirality :  0.042   0.211    686
  Planarity :  0.004   0.037    737
  Dihedral  :  5.864  58.974    664
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.85 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.21 (0.37), residues: 544
  helix:  2.92 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop :  0.58 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 446 
 TYR   0.008   0.001   TYR A 194 
 PHE   0.009   0.001   PHE A 198 
 TRP   0.004   0.001   TRP A 565 
 HIS   0.003   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 4380)
  covalent geometry    : angle       0.54439 ( 5959)
  SS BOND              : bond        0.00221 (    6)
  SS BOND              : angle       1.03729 (   12)
  hydrogen bonds       : bond        0.03808 (  282)
  hydrogen bonds       : angle       3.91334 (  822)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  182 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9107 (mp)
REVERT: A  350 LYS cc_start: 0.9216 (ttpp) cc_final: 0.8982 (ttpp)
REVERT: A  353 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8342 (mt-10)
  outliers start: 14
  outliers final: 7
  residues processed: 52
  average time/residue: 0.6034
  time to fit residues: 32.5289
Evaluate side-chains
  47 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  540 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 42 optimal weight:    0.0000
   chunk 52 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.077222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.058092 restraints weight = 10750.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 3.15
r_work: 0.2730 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4386  Z= 0.134
  Angle     :  0.558   8.352   5971  Z= 0.269
  Chirality :  0.042   0.209    686
  Planarity :  0.004   0.036    737
  Dihedral  :  5.894  59.374    664
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.49 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.17 (0.37), residues: 544
  helix:  2.94 (0.27), residues: 357
  sheet:  None (None), residues: 0
  loop :  0.45 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 590 
 TYR   0.007   0.001   TYR A 194 
 PHE   0.009   0.001   PHE A 198 
 TRP   0.003   0.001   TRP A 626 
 HIS   0.002   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4380)
  covalent geometry    : angle       0.55718 ( 5959)
  SS BOND              : bond        0.00218 (    6)
  SS BOND              : angle       0.79563 (   12)
  hydrogen bonds       : bond        0.03627 (  282)
  hydrogen bonds       : angle       3.91643 (  822)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  197 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8607 (m-30)
REVERT: A  350 LYS cc_start: 0.9205 (ttpp) cc_final: 0.8966 (ttpp)
REVERT: A  353 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8341 (mt-10)
  outliers start: 16
  outliers final: 7
  residues processed: 51
  average time/residue: 0.5448
  time to fit residues: 28.8829
Evaluate side-chains
  50 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  540 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 39 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 349 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.076080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.056819 restraints weight = 10803.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 3.15
r_work: 0.2699 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4386  Z= 0.172
  Angle     :  0.609   7.355   5971  Z= 0.293
  Chirality :  0.043   0.207    686
  Planarity :  0.004   0.037    737
  Dihedral  :  6.070  59.436    664
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 15.85 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  3.17 (0.37), residues: 544
  helix:  2.95 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop :  0.43 (0.47), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 590 
 TYR   0.008   0.001   TYR A 194 
 PHE   0.011   0.001   PHE A 198 
 TRP   0.004   0.001   TRP A 257 
 HIS   0.003   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 4380)
  covalent geometry    : angle       0.60552 ( 5959)
  SS BOND              : bond        0.00398 (    6)
  SS BOND              : angle       1.48547 (   12)
  hydrogen bonds       : bond        0.03998 (  282)
  hydrogen bonds       : angle       3.98566 (  822)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  197 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8537 (m-30)
REVERT: A  350 LYS cc_start: 0.9219 (ttpp) cc_final: 0.8992 (ttpp)
REVERT: A  353 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8287 (mt-10)
REVERT: A  510 SER cc_start: 0.9151 (m) cc_final: 0.8924 (t)
  outliers start: 18
  outliers final: 8
  residues processed: 53
  average time/residue: 0.5513
  time to fit residues: 30.3376
Evaluate side-chains
  49 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  540 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 41 optimal weight:   10.0000
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 364 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.076587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.057480 restraints weight = 10794.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 3.10
r_work: 0.2720 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4386  Z= 0.137
  Angle     :  0.577   8.214   5971  Z= 0.279
  Chirality :  0.042   0.205    686
  Planarity :  0.004   0.039    737
  Dihedral  :  6.062  59.150    664
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.92 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  3.13 (0.37), residues: 544
  helix:  2.96 (0.28), residues: 356
  sheet:  None (None), residues: 0
  loop :  0.34 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 590 
 TYR   0.008   0.001   TYR A 194 
 PHE   0.008   0.001   PHE A 198 
 TRP   0.003   0.001   TRP A 257 
 HIS   0.002   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4380)
  covalent geometry    : angle       0.57446 ( 5959)
  SS BOND              : bond        0.00291 (    6)
  SS BOND              : angle       1.28802 (   12)
  hydrogen bonds       : bond        0.03657 (  282)
  hydrogen bonds       : angle       3.89598 (  822)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  350 LYS cc_start: 0.9214 (ttpp) cc_final: 0.8974 (ttpp)
REVERT: A  353 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8309 (mt-10)
REVERT: A  426 GLU cc_start: 0.8790 (mp0) cc_final: 0.8113 (mp0)
REVERT: A  510 SER cc_start: 0.9161 (m) cc_final: 0.8955 (t)
  outliers start: 13
  outliers final: 7
  residues processed: 50
  average time/residue: 0.5378
  time to fit residues: 27.9057
Evaluate side-chains
  49 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  540 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0770
   chunk 43 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    0.2980
   chunk 42 optimal weight:    0.0970
   chunk 2 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.3536

-------------------------------------------------------------------------------
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 = 0.3322 r_free = 0.3322 target = 0.078142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.059291 restraints weight = 10719.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 3.11
r_work: 0.2755 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4386  Z= 0.110
  Angle     :  0.552   8.557   5971  Z= 0.268
  Chirality :  0.041   0.200    686
  Planarity :  0.004   0.041    737
  Dihedral  :  5.989  59.556    664
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.77 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.17 (0.37), residues: 544
  helix:  2.98 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop :  0.38 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 446 
 TYR   0.007   0.001   TYR A  48 
 PHE   0.009   0.001   PHE A 310 
 TRP   0.003   0.001   TRP A 253 
 HIS   0.001   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 4380)
  covalent geometry    : angle       0.55113 ( 5959)
  SS BOND              : bond        0.00253 (    6)
  SS BOND              : angle       0.99779 (   12)
  hydrogen bonds       : bond        0.03313 (  282)
  hydrogen bonds       : angle       3.81254 (  822)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  197 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8566 (m-30)
REVERT: A  350 LYS cc_start: 0.9197 (ttpp) cc_final: 0.8946 (ttpp)
REVERT: A  353 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8272 (mt-10)
REVERT: A  426 GLU cc_start: 0.8740 (mp0) cc_final: 0.8075 (mp0)
REVERT: A  510 SER cc_start: 0.9147 (m) cc_final: 0.8944 (t)
  outliers start: 11
  outliers final: 6
  residues processed: 49
  average time/residue: 0.5534
  time to fit residues: 28.1914
Evaluate side-chains
  48 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  448 CYS
Chi-restraints excluded: chain A residue  501 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3306 r_free = 0.3306 target = 0.077016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.058020 restraints weight = 10906.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 3.09
r_work: 0.2730 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4386  Z= 0.134
  Angle     :  0.593  11.721   5971  Z= 0.281
  Chirality :  0.041   0.198    686
  Planarity :  0.004   0.045    737
  Dihedral  :  5.897  57.828    664
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.77 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.17 (0.37), residues: 544
  helix:  2.98 (0.28), residues: 356
  sheet:  None (None), residues: 0
  loop :  0.38 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 590 
 TYR   0.007   0.001   TYR A 194 
 PHE   0.008   0.001   PHE A 198 
 TRP   0.003   0.001   TRP A 257 
 HIS   0.002   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4380)
  covalent geometry    : angle       0.59245 ( 5959)
  SS BOND              : bond        0.00264 (    6)
  SS BOND              : angle       0.95546 (   12)
  hydrogen bonds       : bond        0.03536 (  282)
  hydrogen bonds       : angle       3.85541 (  822)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  197 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8519 (m-30)
REVERT: A  350 LYS cc_start: 0.9193 (ttpp) cc_final: 0.8946 (ttpp)
REVERT: A  353 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8283 (mt-10)
REVERT: A  426 GLU cc_start: 0.8745 (mp0) cc_final: 0.8081 (mp0)
REVERT: A  510 SER cc_start: 0.9149 (m) cc_final: 0.8945 (t)
  outliers start: 10
  outliers final: 6
  residues processed: 50
  average time/residue: 0.5765
  time to fit residues: 29.9531
Evaluate side-chains
  50 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  448 CYS
Chi-restraints excluded: chain A residue  501 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.077091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.057950 restraints weight = 10755.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 3.15
r_work: 0.2734 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4386  Z= 0.132
  Angle     :  0.600  11.401   5971  Z= 0.285
  Chirality :  0.041   0.197    686
  Planarity :  0.004   0.046    737
  Dihedral  :  5.829  57.219    664
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.99 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.20 (0.37), residues: 544
  helix:  2.98 (0.27), residues: 357
  sheet:  None (None), residues: 0
  loop :  0.43 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 590 
 TYR   0.007   0.001   TYR A 194 
 PHE   0.008   0.001   PHE A 198 
 TRP   0.003   0.001   TRP A 257 
 HIS   0.002   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4380)
  covalent geometry    : angle       0.59958 ( 5959)
  SS BOND              : bond        0.00240 (    6)
  SS BOND              : angle       0.89774 (   12)
  hydrogen bonds       : bond        0.03578 (  282)
  hydrogen bonds       : angle       3.86066 (  822)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  197 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8521 (m-30)
REVERT: A  350 LYS cc_start: 0.9191 (ttpp) cc_final: 0.8943 (ttpp)
REVERT: A  353 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8274 (mt-10)
REVERT: A  426 GLU cc_start: 0.8769 (mp0) cc_final: 0.8062 (mp0)
REVERT: A  510 SER cc_start: 0.9175 (m) cc_final: 0.8965 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 48
  average time/residue: 0.5945
  time to fit residues: 29.5503
Evaluate side-chains
  47 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  501 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3312 r_free = 0.3312 target = 0.077190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.058584 restraints weight = 10725.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.2890 rms_B_bonded: 3.05
r_work: 0.2761 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4386  Z= 0.137
  Angle     :  0.594  11.324   5971  Z= 0.286
  Chirality :  0.041   0.196    686
  Planarity :  0.004   0.047    737
  Dihedral  :  5.770  56.388    664
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 18.42 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.14 (0.37), residues: 544
  helix:  2.95 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop :  0.40 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 590 
 TYR   0.007   0.001   TYR A 194 
 PHE   0.008   0.001   PHE A 198 
 TRP   0.003   0.001   TRP A 257 
 HIS   0.002   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4380)
  covalent geometry    : angle       0.59365 ( 5959)
  SS BOND              : bond        0.00245 (    6)
  SS BOND              : angle       0.89739 (   12)
  hydrogen bonds       : bond        0.03629 (  282)
  hydrogen bonds       : angle       3.88404 (  822)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1547.81 seconds
wall clock time: 27 minutes 8.85 seconds (1628.85 seconds total)