Starting phenix.real_space_refine
on Fri Aug 22 14:48:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hfe_34718/08_2025/8hfe_34718.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hfe_34718/08_2025/8hfe_34718.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hfe_34718/08_2025/8hfe_34718.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hfe_34718/08_2025/8hfe_34718.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hfe_34718/08_2025/8hfe_34718.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hfe_34718/08_2025/8hfe_34718.cif"
  }
  resolution = 2.5
  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=   0.130
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      20      5.16       5
     Cl      1      4.86       5
     C    2948      2.51       5
     N     682      2.21       5
     O     762      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4413
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 548, 4390
          Classifications: {'peptide': 548}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 528}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 23
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1, 'water': 22}
          Link IDs: {None: 22}
  Time building chain proxies: 1.12, per 1000 atoms: 0.25
  Number of scatterers: 4413
  At special positions: 0
  Unit cell: (70.3625, 71.445, 99.59, 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)
     Cl      1     17.00
     S      20     16.00
     O     762      8.00
     N     682      7.00
     C    2948      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 176 " - pdb=" SG  CYS A 185 " 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: 0.26
  Conformation dependent library (CDL) restraints added in 114.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1010

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 1 sheets defined
      80.1% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 74
      removed outlier: 3.511A  pdb=" N   ASP A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 89
      removed outlier: 3.697A  pdb=" N   VAL A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   PHE A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      Proline residue:  A  83  - end of helix
    Processing helix  chain 'A' and resid 94 through 105
    Processing helix  chain 'A' and resid 105 through 121
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.696A  pdb=" N   ILE A 130 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 166
      removed outlier: 3.839A  pdb=" N   PHE A 150 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE A 156 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 264 through 283
      removed outlier: 3.758A  pdb=" N   THR A 268 " --> pdb=" O   TRP A 264 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      Proline residue:  A 270  - end of helix
      removed outlier: 3.956A  pdb=" N   THR A 283 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.515A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.556A  pdb=" N   LEU A 302 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 320
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 338 through 373
    Processing helix  chain 'A' and resid 385 through 396
      Proline residue:  A 392  - end of helix
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.552A  pdb=" N   ASP A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 440
    Processing helix  chain 'A' and resid 441 through 459
    Processing helix  chain 'A' and resid 464 through 476
      removed outlier: 3.623A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 494
    Processing helix  chain 'A' and resid 497 through 510
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 3.806A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   SER A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 580
    Processing helix  chain 'A' and resid 583 through 593
    Processing helix  chain 'A' and resid 594 through 604
      removed outlier: 3.652A  pdb=" N   HIS A 598 " --> pdb=" O   GLU A 595 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   HIS A 599 " --> pdb=" O   ASN A 596 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 609
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 3.834A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545

    292 hydrogen bonds defined for protein.
    843 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: 0.55

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 649
        1.28 -     1.41: 1336
        1.41 -     1.55: 2516
        1.55 -     1.68: 0
        1.68 -     1.81: 31
  Bond restraints: 4532
  Sorted by residual:
  bond pdb=" C   SER A 480 "
       pdb=" O   SER A 480 "
    ideal  model  delta    sigma   weight residual
    1.236  1.143  0.093 1.19e-02 7.06e+03 6.06e+01
  bond pdb=" C   GLY A 478 "
       pdb=" O   GLY A 478 "
    ideal  model  delta    sigma   weight residual
    1.235  1.145  0.090 1.35e-02 5.49e+03 4.46e+01
  bond pdb=" CA  SER A 480 "
       pdb=" CB  SER A 480 "
    ideal  model  delta    sigma   weight residual
    1.530  1.431  0.099 1.63e-02 3.76e+03 3.70e+01
  bond pdb=" CA  ALA A 477 "
       pdb=" CB  ALA A 477 "
    ideal  model  delta    sigma   weight residual
    1.530  1.472  0.058 9.80e-03 1.04e+04 3.51e+01
  bond pdb=" C   ALA A 476 "
       pdb=" O   ALA A 476 "
    ideal  model  delta    sigma   weight residual
    1.236  1.179  0.057 1.32e-02 5.74e+03 1.87e+01
  ... (remaining 4527 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 6109
        2.51 -     5.02: 61
        5.02 -     7.54: 12
        7.54 -    10.05: 0
       10.05 -    12.56: 1
  Bond angle restraints: 6183
  Sorted by residual:
  angle pdb=" C   GLU A 425 "
        pdb=" N   ALA A 426 "
        pdb=" CA  ALA A 426 "
      ideal   model   delta    sigma   weight residual
     120.38  132.94  -12.56 1.37e+00 5.33e-01 8.41e+01
  angle pdb=" CA  ALA A 426 "
        pdb=" C   ALA A 426 "
        pdb=" O   ALA A 426 "
      ideal   model   delta    sigma   weight residual
     120.63  125.86   -5.23 1.08e+00 8.57e-01 2.34e+01
  angle pdb=" CA  ALA A 477 "
        pdb=" C   ALA A 477 "
        pdb=" N   GLY A 478 "
      ideal   model   delta    sigma   weight residual
     115.78  121.39   -5.61 1.35e+00 5.49e-01 1.72e+01
  angle pdb=" O   PHE A 475 "
        pdb=" C   PHE A 475 "
        pdb=" N   ALA A 476 "
      ideal   model   delta    sigma   weight residual
     122.48  117.47    5.01 1.21e+00 6.83e-01 1.71e+01
  angle pdb=" CA  PHE A 475 "
        pdb=" C   PHE A 475 "
        pdb=" N   ALA A 476 "
      ideal   model   delta    sigma   weight residual
     118.47  123.63   -5.16 1.26e+00 6.30e-01 1.68e+01
  ... (remaining 6178 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.54: 2208
       15.54 -    31.08: 229
       31.08 -    46.62: 71
       46.62 -    62.16: 22
       62.16 -    77.70: 2
  Dihedral angle restraints: 2532
    sinusoidal: 947
      harmonic: 1585
  Sorted by residual:
  dihedral pdb=" CA  ILE A 103 "
           pdb=" C   ILE A 103 "
           pdb=" N   ILE A 104 "
           pdb=" CA  ILE A 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.47  -23.53     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" C   TYR A 205 "
           pdb=" N   TYR A 205 "
           pdb=" CA  TYR A 205 "
           pdb=" CB  TYR A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.76   10.16     0      2.50e+00 1.60e-01 1.65e+01
  dihedral pdb=" N   TYR A 205 "
           pdb=" C   TYR A 205 "
           pdb=" CA  TYR A 205 "
           pdb=" CB  TYR A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.51   -9.71     0      2.50e+00 1.60e-01 1.51e+01
  ... (remaining 2529 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 662
       0.088 -    0.175: 26
       0.175 -    0.263: 2
       0.263 -    0.350: 0
       0.350 -    0.438: 1
  Chirality restraints: 691
  Sorted by residual:
  chirality pdb=" CA  TYR A 205 "
            pdb=" N   TYR A 205 "
            pdb=" C   TYR A 205 "
            pdb=" CB  TYR A 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.79e+00
  chirality pdb=" CA  ILE A 617 "
            pdb=" N   ILE A 617 "
            pdb=" C   ILE A 617 "
            pdb=" CB  ILE A 617 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  SER A 480 "
            pdb=" N   SER A 480 "
            pdb=" C   SER A 480 "
            pdb=" CB  SER A 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.14e-01
  ... (remaining 688 not shown)

  Planarity restraints: 752
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 103 "    0.019 2.00e-02 2.50e+03   3.84e-02 1.47e+01
        pdb=" C   ILE A 103 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   ILE A 103 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ILE A 104 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 475 "    0.012 2.00e-02 2.50e+03   2.25e-02 5.07e+00
        pdb=" C   PHE A 475 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   PHE A 475 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA A 476 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 426 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.53e+00
        pdb=" C   ALA A 426 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ALA A 426 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL A 427 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 749 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 50
        2.65 -     3.21: 4149
        3.21 -     3.77: 7111
        3.77 -     4.34: 10113
        4.34 -     4.90: 16559
  Nonbonded interactions: 37982
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 113 "
            pdb=" O   HOH A 801 "
     model   vdw
     2.082 3.040
  nonbonded pdb=" O   ALA A 384 "
            pdb=" O   HOH A 802 "
     model   vdw
     2.090 3.040
  nonbonded pdb=" O   HOH A 813 "
            pdb=" O   HOH A 822 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" O   HOH A 814 "
            pdb=" O   HOH A 817 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OE2 GLU A 488 "
            pdb=" O   HOH A 803 "
     model   vdw
     2.211 3.040
  ... (remaining 37977 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:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.180
  Find NCS groups from input model:        0.020
  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:7.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
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      :  0.005   0.099   4533  Z= 0.305
  Angle     :  0.664  12.562   6185  Z= 0.404
  Chirality :  0.042   0.438    691
  Planarity :  0.004   0.045    752
  Dihedral  : 14.852  77.702   1519
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.58 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 11.88 %
    Favored  : 87.04 %
  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 aren not related in a simple way.
  whole:  1.37 (0.38), residues: 542
  helix:  1.34 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop :  0.12 (0.53), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 512 
 TYR   0.014   0.001   TYR A  84 
 PHE   0.012   0.001   PHE A 408 
 TRP   0.006   0.001   TRP A 128 
 HIS   0.005   0.001   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 4532)
  covalent geometry    : angle       0.66383 ( 6183)
  SS BOND              : bond        0.00210 (    1)
  SS BOND              : angle       0.85558 (    2)
  hydrogen bonds       : bond        0.14508 (  292)
  hydrogen bonds       : angle       5.75425 (  843)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7653 (mttt)
  outliers start: 5
  outliers final: 4
  residues processed: 56
  average time/residue: 0.5499
  time to fit residues: 31.8850
Evaluate side-chains
  52 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LYS
Chi-restraints excluded: chain A residue  121 ARG
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  350 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0000
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 280 HIS
A 539 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.131006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.107181 restraints weight = 5564.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.71
r_work: 0.3381 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.0962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4533  Z= 0.122
  Angle     :  0.518   7.916   6185  Z= 0.269
  Chirality :  0.040   0.150    691
  Planarity :  0.004   0.038    752
  Dihedral  :  6.375  58.375    603
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.03 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.58 %
    Favored  : 87.04 %
  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 aren not related in a simple way.
  whole:  1.81 (0.38), residues: 542
  helix:  1.62 (0.27), residues: 379
  sheet:  None (None), residues: 0
  loop :  0.37 (0.57), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 442 
 TYR   0.014   0.001   TYR A  84 
 PHE   0.013   0.001   PHE A 110 
 TRP   0.010   0.001   TRP A 128 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 4532)
  covalent geometry    : angle       0.51825 ( 6183)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       0.83606 (    2)
  hydrogen bonds       : bond        0.05073 (  292)
  hydrogen bonds       : angle       4.57497 (  843)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7591 (t70) cc_final: 0.7000 (t70)
REVERT: A  107 MET cc_start: 0.8738 (ttp) cc_final: 0.8479 (ttp)
REVERT: A  254 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7545 (mttt)
REVERT: A  268 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8401 (p)
REVERT: A  459 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7268 (t80)
  outliers start: 11
  outliers final: 5
  residues processed: 60
  average time/residue: 0.4820
  time to fit residues: 30.1171
Evaluate side-chains
  55 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  459 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 19 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0040
   chunk 9 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
A 153 ASN
A 539 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.131133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.106986 restraints weight = 5557.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.74
r_work: 0.3372 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4533  Z= 0.119
  Angle     :  0.498   6.962   6185  Z= 0.260
  Chirality :  0.040   0.160    691
  Planarity :  0.004   0.034    752
  Dihedral  :  5.131  53.135    593
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.03 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 11.88 %
    Favored  : 86.18 %
  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 aren not related in a simple way.
  whole:  2.03 (0.38), residues: 542
  helix:  1.87 (0.27), residues: 378
  sheet:  None (None), residues: 0
  loop :  0.22 (0.55), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 512 
 TYR   0.017   0.001   TYR A  84 
 PHE   0.012   0.001   PHE A 110 
 TRP   0.007   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4532)
  covalent geometry    : angle       0.49784 ( 6183)
  SS BOND              : bond        0.00240 (    1)
  SS BOND              : angle       0.79326 (    2)
  hydrogen bonds       : bond        0.04908 (  292)
  hydrogen bonds       : angle       4.38573 (  843)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7601 (t70) cc_final: 0.7054 (t70)
REVERT: A  121 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8256 (mmt180)
REVERT: A  268 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8447 (p)
REVERT: A  459 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7327 (t80)
REVERT: A  581 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7614 (mt0)
  outliers start: 9
  outliers final: 4
  residues processed: 57
  average time/residue: 0.5065
  time to fit residues: 30.1385
Evaluate side-chains
  54 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ARG
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  459 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 26 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 539 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.131031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.106818 restraints weight = 5523.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.74
r_work: 0.3380 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4533  Z= 0.119
  Angle     :  0.494   6.422   6185  Z= 0.257
  Chirality :  0.040   0.167    691
  Planarity :  0.004   0.033    752
  Dihedral  :  4.965  49.963    593
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.03 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 11.88 %
    Favored  : 85.53 %
  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 aren not related in a simple way.
  whole:  2.10 (0.38), residues: 542
  helix:  1.94 (0.27), residues: 378
  sheet:  None (None), residues: 0
  loop :  0.20 (0.54), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 512 
 TYR   0.017   0.001   TYR A  84 
 PHE   0.012   0.001   PHE A 110 
 TRP   0.007   0.001   TRP A 128 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 4532)
  covalent geometry    : angle       0.49400 ( 6183)
  SS BOND              : bond        0.00269 (    1)
  SS BOND              : angle       0.77209 (    2)
  hydrogen bonds       : bond        0.04868 (  292)
  hydrogen bonds       : angle       4.35956 (  843)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7570 (t70) cc_final: 0.7013 (t70)
REVERT: A  121 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8229 (mmt180)
REVERT: A  254 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7536 (mttt)
REVERT: A  268 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8441 (p)
REVERT: A  389 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8526 (mp)
REVERT: A  459 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7340 (t80)
REVERT: A  581 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7624 (mt0)
  outliers start: 12
  outliers final: 5
  residues processed: 56
  average time/residue: 0.5475
  time to fit residues: 31.8927
Evaluate side-chains
  55 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ARG
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  459 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 539 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.130081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.105726 restraints weight = 5582.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.74
r_work: 0.3349 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4533  Z= 0.127
  Angle     :  0.500   5.855   6185  Z= 0.262
  Chirality :  0.040   0.177    691
  Planarity :  0.004   0.033    752
  Dihedral  :  4.830  46.054    593
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.03 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 12.10 %
    Favored  : 85.31 %
  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 aren not related in a simple way.
  whole:  2.12 (0.37), residues: 542
  helix:  1.96 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop :  0.19 (0.53), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 512 
 TYR   0.018   0.001   TYR A  84 
 PHE   0.012   0.001   PHE A 110 
 TRP   0.007   0.001   TRP A 128 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4532)
  covalent geometry    : angle       0.49950 ( 6183)
  SS BOND              : bond        0.00308 (    1)
  SS BOND              : angle       0.78954 (    2)
  hydrogen bonds       : bond        0.05048 (  292)
  hydrogen bonds       : angle       4.38538 (  843)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7637 (t70) cc_final: 0.7041 (t70)
REVERT: A  121 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8225 (mmt180)
REVERT: A  254 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7628 (mttt)
REVERT: A  268 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8435 (p)
REVERT: A  304 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7397 (mm-30)
REVERT: A  581 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7648 (mt0)
REVERT: A  610 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.6716 (mt0)
  outliers start: 12
  outliers final: 5
  residues processed: 57
  average time/residue: 0.4900
  time to fit residues: 29.0624
Evaluate side-chains
  55 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ARG
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  610 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 539 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.130483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.106330 restraints weight = 5645.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.73
r_work: 0.3347 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4533  Z= 0.129
  Angle     :  0.500   5.847   6185  Z= 0.262
  Chirality :  0.040   0.180    691
  Planarity :  0.004   0.034    752
  Dihedral  :  4.761  42.987    593
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.03 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 12.53 %
    Favored  : 84.88 %
  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 aren not related in a simple way.
  whole:  2.12 (0.38), residues: 542
  helix:  1.96 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop :  0.20 (0.53), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  81 
 TYR   0.020   0.001   TYR A 391 
 PHE   0.017   0.001   PHE A 329 
 TRP   0.007   0.001   TRP A 128 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4532)
  covalent geometry    : angle       0.50026 ( 6183)
  SS BOND              : bond        0.00312 (    1)
  SS BOND              : angle       0.76208 (    2)
  hydrogen bonds       : bond        0.05061 (  292)
  hydrogen bonds       : angle       4.40457 (  843)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7619 (t70) cc_final: 0.7019 (t70)
REVERT: A  100 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8308 (tm)
REVERT: A  121 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8234 (mmt180)
REVERT: A  254 LYS cc_start: 0.7879 (mtmt) cc_final: 0.7648 (mttt)
REVERT: A  268 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8416 (p)
REVERT: A  304 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7368 (mm-30)
REVERT: A  610 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.6768 (mt0)
  outliers start: 12
  outliers final: 6
  residues processed: 57
  average time/residue: 0.4997
  time to fit residues: 29.6205
Evaluate side-chains
  58 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  121 ARG
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  610 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 539 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.130149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.106094 restraints weight = 5553.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.71
r_work: 0.3333 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4533  Z= 0.135
  Angle     :  0.512   6.172   6185  Z= 0.268
  Chirality :  0.041   0.189    691
  Planarity :  0.004   0.034    752
  Dihedral  :  4.700  39.657    593
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.03 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 13.17 %
    Favored  : 84.02 %
  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 aren not related in a simple way.
  whole:  2.12 (0.38), residues: 542
  helix:  1.98 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop :  0.17 (0.53), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.023   0.001   TYR A 391 
 PHE   0.020   0.001   PHE A 329 
 TRP   0.007   0.001   TRP A 128 
 HIS   0.003   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4532)
  covalent geometry    : angle       0.51170 ( 6183)
  SS BOND              : bond        0.00342 (    1)
  SS BOND              : angle       0.82602 (    2)
  hydrogen bonds       : bond        0.05196 (  292)
  hydrogen bonds       : angle       4.41016 (  843)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7706 (t70) cc_final: 0.7096 (t70)
REVERT: A  100 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8344 (tm)
REVERT: A  121 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8281 (mmt180)
REVERT: A  268 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8456 (p)
REVERT: A  610 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.6794 (mt0)
  outliers start: 13
  outliers final: 6
  residues processed: 56
  average time/residue: 0.4799
  time to fit residues: 27.9498
Evaluate side-chains
  56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  121 ARG
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  610 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 15 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 539 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.130570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.106420 restraints weight = 5585.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.72
r_work: 0.3353 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4533  Z= 0.129
  Angle     :  0.512   7.350   6185  Z= 0.266
  Chirality :  0.040   0.196    691
  Planarity :  0.004   0.034    752
  Dihedral  :  4.596  35.511    593
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.21 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.04 %
    Favored  : 84.02 %
  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 aren not related in a simple way.
  whole:  2.13 (0.38), residues: 542
  helix:  2.00 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop :  0.12 (0.53), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  81 
 TYR   0.024   0.001   TYR A 391 
 PHE   0.023   0.001   PHE A 329 
 TRP   0.007   0.001   TRP A 128 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4532)
  covalent geometry    : angle       0.51146 ( 6183)
  SS BOND              : bond        0.00312 (    1)
  SS BOND              : angle       0.78948 (    2)
  hydrogen bonds       : bond        0.05016 (  292)
  hydrogen bonds       : angle       4.39478 (  843)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7641 (t70) cc_final: 0.7039 (t70)
REVERT: A  100 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8317 (tm)
REVERT: A  121 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8249 (mmt180)
REVERT: A  268 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8425 (p)
REVERT: A  610 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.6707 (mt0)
  outliers start: 9
  outliers final: 5
  residues processed: 49
  average time/residue: 0.4644
  time to fit residues: 23.6936
Evaluate side-chains
  50 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  121 ARG
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  610 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 6 optimal weight:    0.0570
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 539 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.132144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.108137 restraints weight = 5601.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 1.71
r_work: 0.3386 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4533  Z= 0.112
  Angle     :  0.492   6.593   6185  Z= 0.254
  Chirality :  0.040   0.205    691
  Planarity :  0.004   0.035    752
  Dihedral  :  4.437  31.955    593
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.03 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.82 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.38), residues: 542
  helix:  2.10 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop :  0.11 (0.53), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 440 
 TYR   0.028   0.001   TYR A 391 
 PHE   0.024   0.001   PHE A 329 
 TRP   0.007   0.001   TRP A 128 
 HIS   0.002   0.000   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 4532)
  covalent geometry    : angle       0.49170 ( 6183)
  SS BOND              : bond        0.00261 (    1)
  SS BOND              : angle       0.75620 (    2)
  hydrogen bonds       : bond        0.04562 (  292)
  hydrogen bonds       : angle       4.30261 (  843)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7567 (t70) cc_final: 0.7054 (t70)
REVERT: A  100 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8284 (tm)
REVERT: A  121 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8196 (mmt180)
REVERT: A  189 LYS cc_start: 0.8385 (mptt) cc_final: 0.7954 (mmtt)
REVERT: A  268 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8399 (p)
REVERT: A  579 SER cc_start: 0.8125 (m) cc_final: 0.7853 (p)
REVERT: A  610 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.6592 (mt0)
  outliers start: 11
  outliers final: 6
  residues processed: 53
  average time/residue: 0.4290
  time to fit residues: 23.7232
Evaluate side-chains
  53 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  121 ARG
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  610 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0270
   chunk 48 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.131450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.107547 restraints weight = 5580.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.71
r_work: 0.3373 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4533  Z= 0.123
  Angle     :  0.509   6.671   6185  Z= 0.263
  Chirality :  0.040   0.210    691
  Planarity :  0.004   0.036    752
  Dihedral  :  4.468  28.906    593
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.21 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.47 %
    Favored  : 83.15 %
  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 aren not related in a simple way.
  whole:  2.21 (0.38), residues: 542
  helix:  2.12 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop :  0.03 (0.53), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 440 
 TYR   0.039   0.001   TYR A 391 
 PHE   0.024   0.001   PHE A 329 
 TRP   0.007   0.001   TRP A 128 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4532)
  covalent geometry    : angle       0.50840 ( 6183)
  SS BOND              : bond        0.00283 (    1)
  SS BOND              : angle       0.76688 (    2)
  hydrogen bonds       : bond        0.04823 (  292)
  hydrogen bonds       : angle       4.35198 (  843)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7634 (t70) cc_final: 0.7106 (t70)
REVERT: A  100 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8299 (tm)
REVERT: A  121 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8207 (mmt180)
REVERT: A  189 LYS cc_start: 0.8385 (mptt) cc_final: 0.7955 (mmtt)
REVERT: A  242 MET cc_start: 0.8544 (mtp) cc_final: 0.8196 (mtm)
REVERT: A  268 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8378 (p)
REVERT: A  459 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7376 (t80)
REVERT: A  579 SER cc_start: 0.8212 (m) cc_final: 0.7950 (p)
REVERT: A  610 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.6598 (mt0)
  outliers start: 11
  outliers final: 6
  residues processed: 54
  average time/residue: 0.4567
  time to fit residues: 25.6181
Evaluate side-chains
  54 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  121 ARG
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  459 PHE
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  610 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0270
   chunk 32 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.7442

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.130760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.106766 restraints weight = 5566.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.71
r_work: 0.3354 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4533  Z= 0.128
  Angle     :  0.512   6.695   6185  Z= 0.265
  Chirality :  0.040   0.208    691
  Planarity :  0.004   0.034    752
  Dihedral  :  4.456  25.843    593
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.58 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.25 %
    Favored  : 83.15 %
  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 aren not related in a simple way.
  whole:  2.19 (0.38), residues: 542
  helix:  2.11 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop :  0.02 (0.53), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  81 
 TYR   0.019   0.001   TYR A  84 
 PHE   0.024   0.001   PHE A 329 
 TRP   0.007   0.001   TRP A 585 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4532)
  covalent geometry    : angle       0.51159 ( 6183)
  SS BOND              : bond        0.00308 (    1)
  SS BOND              : angle       0.79040 (    2)
  hydrogen bonds       : bond        0.04974 (  292)
  hydrogen bonds       : angle       4.37247 (  843)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1506.15 seconds
wall clock time: 26 minutes 21.21 seconds (1581.21 seconds total)