Starting phenix.real_space_refine
on Fri Aug 22 14:00:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8edn_28037/08_2025/8edn_28037.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8edn_28037/08_2025/8edn_28037.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8edn_28037/08_2025/8edn_28037.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8edn_28037/08_2025/8edn_28037.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8edn_28037/08_2025/8edn_28037.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8edn_28037/08_2025/8edn_28037.map"
  }
  resolution = 3.8
  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=   0.003
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      13      5.16       5
     C    2360      2.51       5
     N     662      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3683
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 579, 3683
          Classifications: {'peptide': 579}
          Incomplete info: {'truncation_to_alanine': 309}
          Link IDs: {'PTRANS': 21, 'TRANS': 557}
          Chain breaks: 8
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 977
          Unresolved non-hydrogen angles: 1225
          Unresolved non-hydrogen dihedrals: 770
          Unresolved non-hydrogen chiralities: 101
          Planarities with less than four sites: {'PHE:plan': 7, 'ASN:plan1': 22, 'ARG:plan': 14, 'GLU:plan': 30, 'TYR:plan': 2, 'GLN:plan1': 18, 'ASP:plan': 24, 'HIS:plan': 4, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 485
  Time building chain proxies: 0.91, per 1000 atoms: 0.25
  Number of scatterers: 3683
  At special positions: 0
  Unit cell: (97.76, 80.08, 81.12, 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      13     16.00
     O     648      8.00
     N     662      7.00
     C    2360      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.33
  Conformation dependent library (CDL) restraints added in 129.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1134

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 0 sheets defined
      81.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 51 through 67
    Processing helix  chain 'A' and resid 72 through 97
      removed outlier: 4.121A  pdb=" N   GLU A  76 " --> pdb=" O   GLY A  72 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LYS A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 105
      removed outlier: 6.283A  pdb=" N   ARG A 103 " --> pdb=" O   ASP A 100 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   LEU A 104 " --> pdb=" O   THR A 101 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ASP A 105 " --> pdb=" O   MET A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 117
      Proline residue:  A 115  - end of helix
    Processing helix  chain 'A' and resid 130 through 147
      removed outlier: 3.629A  pdb=" N   CYS A 147 " --> pdb=" O   PHE A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 167
      removed outlier: 3.681A  pdb=" N   VAL A 153 " --> pdb=" O   ASN A 149 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL A 166 " --> pdb=" O   GLN A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 182
      removed outlier: 3.619A  pdb=" N   TYR A 182 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 201
    Processing helix  chain 'A' and resid 205 through 227
      removed outlier: 3.649A  pdb=" N   LYS A 218 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 237
      removed outlier: 3.636A  pdb=" N   TYR A 235 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 256
    Processing helix  chain 'A' and resid 259 through 276
      Proline residue:  A 268  - end of helix
      removed outlier: 3.554A  pdb=" N   ILE A 272 " --> pdb=" O   PRO A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 286
      removed outlier: 3.887A  pdb=" N   SER A 285 " --> pdb=" O   ILE A 281 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LYS A 286 " --> pdb=" O   GLN A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 292
      No H-bonds generated for 'chain 'A' and resid 290 through 292'
    Processing helix  chain 'A' and resid 293 through 308
    Processing helix  chain 'A' and resid 314 through 334
    Processing helix  chain 'A' and resid 341 through 358
      removed outlier: 3.964A  pdb=" N   MET A 349 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   VAL A 351 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   ASP A 352 " --> pdb=" O   SER A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 387
    Processing helix  chain 'A' and resid 391 through 398
    Processing helix  chain 'A' and resid 403 through 419
    Processing helix  chain 'A' and resid 432 through 434
      No H-bonds generated for 'chain 'A' and resid 432 through 434'
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 3.545A  pdb=" N   PHE A 443 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 503
    Processing helix  chain 'A' and resid 515 through 520
    Processing helix  chain 'A' and resid 521 through 533
      removed outlier: 3.661A  pdb=" N   LEU A 532 " --> pdb=" O   GLY A 528 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   VAL A 533 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 553
      removed outlier: 3.520A  pdb=" N   ALA A 542 " --> pdb=" O   MET A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 565 through 588
    Processing helix  chain 'A' and resid 592 through 618
    Processing helix  chain 'A' and resid 678 through 697
      removed outlier: 3.884A  pdb=" N   TRP A 696 " --> pdb=" O   TYR A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 721
      removed outlier: 4.479A  pdb=" N   LEU A 704 " --> pdb=" O   THR A 700 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    945 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: 0.38

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1249
        1.34 -     1.46: 505
        1.46 -     1.58: 1976
        1.58 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 3748
  Sorted by residual:
  bond pdb=" N   ARG A 304 "
       pdb=" CA  ARG A 304 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.29e-02 6.01e+03 6.30e+00
  bond pdb=" N   ASP A 301 "
       pdb=" CA  ASP A 301 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.17e-02 7.31e+03 6.08e+00
  bond pdb=" N   SER A 302 "
       pdb=" CA  SER A 302 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.028 1.17e-02 7.31e+03 5.91e+00
  bond pdb=" N   LEU A 303 "
       pdb=" CA  LEU A 303 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.16e-02 7.43e+03 5.58e+00
  bond pdb=" N   PHE A 299 "
       pdb=" CA  PHE A 299 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.19e-02 7.06e+03 5.35e+00
  ... (remaining 3743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 5118
        2.52 -     5.03: 37
        5.03 -     7.55: 3
        7.55 -    10.07: 2
       10.07 -    12.59: 1
  Bond angle restraints: 5161
  Sorted by residual:
  angle pdb=" C   LYS A 305 "
        pdb=" N   ALA A 306 "
        pdb=" CA  ALA A 306 "
      ideal   model   delta    sigma   weight residual
     120.38  112.49    7.89 1.46e+00 4.69e-01 2.92e+01
  angle pdb=" N   VAL A 432 "
        pdb=" CA  VAL A 432 "
        pdb=" C   VAL A 432 "
      ideal   model   delta    sigma   weight residual
     113.47  108.34    5.13 1.01e+00 9.80e-01 2.58e+01
  angle pdb=" CB  MET A 546 "
        pdb=" CG  MET A 546 "
        pdb=" SD  MET A 546 "
      ideal   model   delta    sigma   weight residual
     112.70  100.11   12.59 3.00e+00 1.11e-01 1.76e+01
  angle pdb=" CA  LYS A 305 "
        pdb=" C   LYS A 305 "
        pdb=" O   LYS A 305 "
      ideal   model   delta    sigma   weight residual
     121.07  116.94    4.13 1.10e+00 8.26e-01 1.41e+01
  angle pdb=" CA  LYS A 305 "
        pdb=" C   LYS A 305 "
        pdb=" N   ALA A 306 "
      ideal   model   delta    sigma   weight residual
     116.79  120.98   -4.19 1.28e+00 6.10e-01 1.07e+01
  ... (remaining 5156 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.46: 1963
       11.46 -    22.93: 148
       22.93 -    34.39: 55
       34.39 -    45.85: 17
       45.85 -    57.31: 3
  Dihedral angle restraints: 2186
    sinusoidal: 472
      harmonic: 1714
  Sorted by residual:
  dihedral pdb=" CA  LYS A 218 "
           pdb=" C   LYS A 218 "
           pdb=" N   ALA A 219 "
           pdb=" CA  ALA A 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.97   15.03     0      5.00e+00 4.00e-02 9.04e+00
  dihedral pdb=" CA  GLN A 576 "
           pdb=" CB  GLN A 576 "
           pdb=" CG  GLN A 576 "
           pdb=" CD  GLN A 576 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.55   41.55     3      1.50e+01 4.44e-03 7.44e+00
  dihedral pdb=" N   PHE A 299 "
           pdb=" CA  PHE A 299 "
           pdb=" CB  PHE A 299 "
           pdb=" CG  PHE A 299 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  138.69   41.31     3      1.50e+01 4.44e-03 7.39e+00
  ... (remaining 2183 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 467
       0.034 -    0.067: 140
       0.067 -    0.101: 35
       0.101 -    0.134: 6
       0.134 -    0.168: 2
  Chirality restraints: 650
  Sorted by residual:
  chirality pdb=" CA  LEU A 300 "
            pdb=" N   LEU A 300 "
            pdb=" C   LEU A 300 "
            pdb=" CB  LEU A 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.03e-01
  chirality pdb=" CA  LEU A 303 "
            pdb=" N   LEU A 303 "
            pdb=" C   LEU A 303 "
            pdb=" CB  LEU A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.14 2.00e-01 2.50e+01 5.24e-01
  chirality pdb=" CA  LYS A 305 "
            pdb=" N   LYS A 305 "
            pdb=" C   LYS A 305 "
            pdb=" CB  LYS A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.97e-01
  ... (remaining 647 not shown)

  Planarity restraints: 670
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 218 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.30e+00
        pdb=" C   LYS A 218 "    0.020 2.00e-02 2.50e+03
        pdb=" O   LYS A 218 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ALA A 219 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 676 "    0.016 5.00e-02 4.00e+02   2.47e-02 9.80e-01
        pdb=" N   PRO A 677 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO A 677 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 677 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 677 "   -0.016 5.00e-02 4.00e+02   2.41e-02 9.26e-01
        pdb=" N   PRO A 678 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 678 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 678 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 667 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 364
        2.74 -     3.28: 3962
        3.28 -     3.82: 6422
        3.82 -     4.36: 6359
        4.36 -     4.90: 10953
  Nonbonded interactions: 28060
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 440 "
            pdb=" O   CYS A 509 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O   PHE A 443 "
            pdb=" OG1 THR A 446 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   LYS A 584 "
            pdb=" OG  SER A 587 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" NE2 HIS A 501 "
            pdb=" O   GLU A 544 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" OH  TYR A 235 "
            pdb=" O   ILE A 275 "
     model   vdw
     2.346 3.040
  ... (remaining 28055 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.270
  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:                    0.000
  Process input model:                     4.460
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6114
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      :  0.002   0.032   3748  Z= 0.156
  Angle     :  0.579  12.587   5161  Z= 0.342
  Chirality :  0.036   0.168    650
  Planarity :  0.003   0.029    670
  Dihedral  : 11.311  57.314   1052
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.70 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  0.92 %
    Favored  : 98.62 %
  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:  2.77 (0.37), residues: 561
  helix:  2.78 (0.25), residues: 418
  sheet:  None (None), residues: 0
  loop : -1.19 (0.58), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 601 
 TYR   0.010   0.001   TYR A 408 
 PHE   0.016   0.001   PHE A 250 
 TRP   0.009   0.001   TRP A 425 
 HIS   0.006   0.001   HIS A 393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3748)
  covalent geometry    : angle       0.57926 ( 5161)
  hydrogen bonds       : bond        0.12972 (  321)
  hydrogen bonds       : angle       4.73594 (  945)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 ASN cc_start: 0.8178 (t0) cc_final: 0.7625 (t0)
REVERT: A  598 LYS cc_start: 0.8428 (mttm) cc_final: 0.8047 (mtpt)
  outliers start: 1
  outliers final: 1
  residues processed: 102
  average time/residue: 0.0580
  time to fit residues: 7.1994
Evaluate side-chains
  50 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0270
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   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 415 HIS
A 510 ASN
A 614 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.109189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.091556 restraints weight = 15152.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.092944 restraints weight = 11200.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.093772 restraints weight = 8916.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.094706 restraints weight = 7654.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.095178 restraints weight = 6722.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3748  Z= 0.124
  Angle     :  0.545  11.220   5161  Z= 0.283
  Chirality :  0.036   0.144    650
  Planarity :  0.006   0.123    670
  Dihedral  :  4.020  37.494    589
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.46 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.21 %
    Favored  : 82.03 %
  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:  2.69 (0.38), residues: 561
  helix:  2.58 (0.25), residues: 440
  sheet:  None (None), residues: 0
  loop : -1.43 (0.63), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 601 
 TYR   0.007   0.001   TYR A 227 
 PHE   0.030   0.003   PHE A 570 
 TRP   0.009   0.001   TRP A 561 
 HIS   0.007   0.002   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3748)
  covalent geometry    : angle       0.54518 ( 5161)
  hydrogen bonds       : bond        0.03483 (  321)
  hydrogen bonds       : angle       3.71981 (  945)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A  579 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.6327 (t80)
REVERT: A  684 GLN cc_start: 0.7801 (tp40) cc_final: 0.7566 (mm-40)
  outliers start: 6
  outliers final: 3
  residues processed: 62
  average time/residue: 0.0447
  time to fit residues: 3.7127
Evaluate side-chains
  50 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  393 HIS
Chi-restraints excluded: chain A residue  448 HIS
Chi-restraints excluded: chain A residue  579 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0070
   chunk 23 optimal weight:    0.0030
   chunk 41 optimal weight:    6.9990
   overall best weight:    0.4408

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

Flipped N/Q/H residues before XYZ refinement:
A 415 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.109030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.091176 restraints weight = 15236.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.092620 restraints weight = 11381.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.093690 restraints weight = 9123.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.094477 restraints weight = 7687.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.094675 restraints weight = 6749.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6696
moved from start:          0.3516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3748  Z= 0.109
  Angle     :  0.524   9.341   5161  Z= 0.271
  Chirality :  0.035   0.128    650
  Planarity :  0.005   0.082    670
  Dihedral  :  3.511  16.319    587
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.74 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 16.59 %
    Favored  : 78.80 %
  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:  2.71 (0.37), residues: 561
  helix:  2.62 (0.25), residues: 444
  sheet:  None (None), residues: 0
  loop : -1.67 (0.60), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 601 
 TYR   0.005   0.001   TYR A 227 
 PHE   0.035   0.002   PHE A 579 
 TRP   0.010   0.001   TRP A 561 
 HIS   0.007   0.001   HIS A 553 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 3748)
  covalent geometry    : angle       0.52412 ( 5161)
  hydrogen bonds       : bond        0.03188 (  321)
  hydrogen bonds       : angle       3.51666 (  945)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: A  408 TYR cc_start: 0.6725 (t80) cc_final: 0.6486 (t80)
REVERT: A  598 LYS cc_start: 0.8554 (mttt) cc_final: 0.8072 (mttp)
REVERT: A  602 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7609 (mm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 64
  average time/residue: 0.0545
  time to fit residues: 4.4797
Evaluate side-chains
  51 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  393 HIS
Chi-restraints excluded: chain A residue  448 HIS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  530 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0970
   chunk 40 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
A 415 HIS
A 614 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.106559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.088426 restraints weight = 15335.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.089849 restraints weight = 11181.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.090750 restraints weight = 8904.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.091256 restraints weight = 7606.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.091976 restraints weight = 6886.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
moved from start:          0.4648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3748  Z= 0.115
  Angle     :  0.550  11.402   5161  Z= 0.280
  Chirality :  0.035   0.140    650
  Planarity :  0.004   0.041    670
  Dihedral  :  3.532  15.842    587
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.28 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.51 %
    Favored  : 79.26 %
  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:  2.69 (0.36), residues: 561
  helix:  2.59 (0.24), residues: 444
  sheet:  None (None), residues: 0
  loop : -1.60 (0.57), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 601 
 TYR   0.009   0.001   TYR A 333 
 PHE   0.013   0.002   PHE A 143 
 TRP   0.015   0.001   TRP A 561 
 HIS   0.006   0.001   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 3748)
  covalent geometry    : angle       0.55035 ( 5161)
  hydrogen bonds       : bond        0.03256 (  321)
  hydrogen bonds       : angle       3.43685 (  945)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: A  558 ILE cc_start: 0.8721 (mm) cc_final: 0.8414 (mm)
REVERT: A  571 TRP cc_start: 0.6854 (m-90) cc_final: 0.6496 (m100)
REVERT: A  601 ARG cc_start: 0.8311 (ptp90) cc_final: 0.7916 (ptp90)
  outliers start: 7
  outliers final: 4
  residues processed: 63
  average time/residue: 0.0502
  time to fit residues: 3.9945
Evaluate side-chains
  51 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  448 HIS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  530 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 4 optimal weight:    0.3980
   chunk 34 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   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 393 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.105100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.086737 restraints weight = 15372.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.088169 restraints weight = 11067.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.089236 restraints weight = 8796.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.089579 restraints weight = 7390.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.090434 restraints weight = 6774.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.5437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3748  Z= 0.106
  Angle     :  0.526   9.605   5161  Z= 0.264
  Chirality :  0.035   0.141    650
  Planarity :  0.003   0.037    670
  Dihedral  :  3.469  15.204    587
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.46 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.05 %
    Favored  : 79.26 %
  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:  2.71 (0.37), residues: 561
  helix:  2.62 (0.25), residues: 443
  sheet:  None (None), residues: 0
  loop : -1.66 (0.56), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 607 
 TYR   0.014   0.001   TYR A 491 
 PHE   0.017   0.002   PHE A 570 
 TRP   0.017   0.001   TRP A 599 
 HIS   0.004   0.001   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 3748)
  covalent geometry    : angle       0.52575 ( 5161)
  hydrogen bonds       : bond        0.03070 (  321)
  hydrogen bonds       : angle       3.40288 (  945)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  556 ASP cc_start: 0.7929 (p0) cc_final: 0.7378 (m-30)
  outliers start: 8
  outliers final: 4
  residues processed: 54
  average time/residue: 0.0408
  time to fit residues: 3.0185
Evaluate side-chains
  49 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  448 HIS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  530 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0370
   chunk 45 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0040
   chunk 51 optimal weight:    1.9990
   chunk 28 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7674

-------------------------------------------------------------------------------
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 = 0.4028 r_free = 0.4028 target = 0.103935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.085455 restraints weight = 15506.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.086908 restraints weight = 11196.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.087652 restraints weight = 8904.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.088653 restraints weight = 7675.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.089044 restraints weight = 6760.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.6080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3748  Z= 0.109
  Angle     :  0.566  13.973   5161  Z= 0.281
  Chirality :  0.036   0.128    650
  Planarity :  0.003   0.037    670
  Dihedral  :  3.466  15.394    587
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.10 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 18.89 %
    Favored  : 77.88 %
  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:  2.71 (0.37), residues: 561
  helix:  2.59 (0.24), residues: 445
  sheet:  None (None), residues: 0
  loop : -1.59 (0.58), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 607 
 TYR   0.010   0.001   TYR A 491 
 PHE   0.019   0.002   PHE A 358 
 TRP   0.023   0.001   TRP A 561 
 HIS   0.003   0.001   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 3748)
  covalent geometry    : angle       0.56553 ( 5161)
  hydrogen bonds       : bond        0.03198 (  321)
  hydrogen bonds       : angle       3.43735 (  945)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 LYS cc_start: 0.8718 (mttt) cc_final: 0.8250 (mttp)
  outliers start: 7
  outliers final: 6
  residues processed: 49
  average time/residue: 0.0456
  time to fit residues: 3.0640
Evaluate side-chains
  46 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  448 HIS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  501 HIS
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  546 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0020
   chunk 51 optimal weight:    0.9990
   chunk 6 optimal weight:    0.1980
   chunk 33 optimal weight:    0.0670
   chunk 52 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0270
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    0.2184

-------------------------------------------------------------------------------
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 = 0.4044 r_free = 0.4044 target = 0.105255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.086920 restraints weight = 15908.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.088430 restraints weight = 11490.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.089215 restraints weight = 9046.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.090242 restraints weight = 7772.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.090692 restraints weight = 6800.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.6280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3748  Z= 0.098
  Angle     :  0.543  12.243   5161  Z= 0.268
  Chirality :  0.034   0.119    650
  Planarity :  0.003   0.036    670
  Dihedral  :  3.389  15.569    587
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.10 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.89 %
    Favored  : 78.80 %
  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:  2.84 (0.37), residues: 561
  helix:  2.77 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop : -1.67 (0.57), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 601 
 TYR   0.011   0.001   TYR A 491 
 PHE   0.012   0.001   PHE A 570 
 TRP   0.019   0.001   TRP A 561 
 HIS   0.003   0.001   HIS A 553 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 3748)
  covalent geometry    : angle       0.54324 ( 5161)
  hydrogen bonds       : bond        0.02916 (  321)
  hydrogen bonds       : angle       3.25614 (  945)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASN cc_start: 0.8166 (m110) cc_final: 0.7949 (m-40)
REVERT: A  558 ILE cc_start: 0.8732 (mm) cc_final: 0.8439 (mm)
REVERT: A  571 TRP cc_start: 0.6248 (m-10) cc_final: 0.6015 (m-10)
REVERT: A  598 LYS cc_start: 0.8686 (mttt) cc_final: 0.8207 (mttp)
  outliers start: 5
  outliers final: 4
  residues processed: 57
  average time/residue: 0.0563
  time to fit residues: 4.1062
Evaluate side-chains
  50 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  448 HIS
Chi-restraints excluded: chain A residue  501 HIS
Chi-restraints excluded: chain A residue  530 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0370
   chunk 36 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0980
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.104067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.085696 restraints weight = 15661.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.087240 restraints weight = 11235.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.088316 restraints weight = 8817.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.088832 restraints weight = 7444.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.089574 restraints weight = 6705.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.6743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3748  Z= 0.100
  Angle     :  0.560  10.788   5161  Z= 0.274
  Chirality :  0.035   0.119    650
  Planarity :  0.004   0.043    670
  Dihedral  :  3.370  16.123    587
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.74 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 18.43 %
    Favored  : 78.34 %
  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:  2.99 (0.37), residues: 561
  helix:  2.85 (0.24), residues: 434
  sheet:  None (None), residues: 0
  loop : -1.33 (0.57), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 681 
 TYR   0.012   0.001   TYR A 408 
 PHE   0.016   0.001   PHE A 358 
 TRP   0.019   0.001   TRP A 561 
 HIS   0.002   0.001   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 3748)
  covalent geometry    : angle       0.56036 ( 5161)
  hydrogen bonds       : bond        0.03018 (  321)
  hydrogen bonds       : angle       3.24678 (  945)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A  556 ASP cc_start: 0.8117 (p0) cc_final: 0.7537 (m-30)
REVERT: A  558 ILE cc_start: 0.8772 (mm) cc_final: 0.8475 (mm)
REVERT: A  571 TRP cc_start: 0.6282 (m-10) cc_final: 0.6063 (m-10)
REVERT: A  602 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7680 (mm-30)
REVERT: A  681 ARG cc_start: 0.7387 (ptm-80) cc_final: 0.6735 (ptm-80)
  outliers start: 7
  outliers final: 5
  residues processed: 53
  average time/residue: 0.0543
  time to fit residues: 3.8225
Evaluate side-chains
  49 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  448 HIS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  501 HIS
Chi-restraints excluded: chain A residue  530 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0670
   chunk 55 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7320

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

Flipped N/Q/H residues before XYZ refinement:
A 712 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.103341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.085205 restraints weight = 15857.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.086650 restraints weight = 11446.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.087753 restraints weight = 9073.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 16)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.088273 restraints weight = 7646.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.088978 restraints weight = 6887.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.7161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3748  Z= 0.108
  Angle     :  0.574   9.861   5161  Z= 0.282
  Chirality :  0.035   0.122    650
  Planarity :  0.003   0.038    670
  Dihedral  :  3.454  16.816    587
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.10 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.82 %
    Favored  : 76.96 %
  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:  2.87 (0.37), residues: 561
  helix:  2.68 (0.25), residues: 439
  sheet:  None (None), residues: 0
  loop : -1.21 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 681 
 TYR   0.009   0.001   TYR A 491 
 PHE   0.024   0.002   PHE A 579 
 TRP   0.034   0.002   TRP A 267 
 HIS   0.003   0.001   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 3748)
  covalent geometry    : angle       0.57377 ( 5161)
  hydrogen bonds       : bond        0.03037 (  321)
  hydrogen bonds       : angle       3.34069 (  945)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: A  556 ASP cc_start: 0.8031 (p0) cc_final: 0.7628 (m-30)
REVERT: A  558 ILE cc_start: 0.8736 (mm) cc_final: 0.8435 (mm)
REVERT: A  571 TRP cc_start: 0.6280 (m-10) cc_final: 0.6014 (m-10)
  outliers start: 7
  outliers final: 7
  residues processed: 51
  average time/residue: 0.0362
  time to fit residues: 2.5686
Evaluate side-chains
  50 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  448 HIS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  501 HIS
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  693 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0370
   chunk 5 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0770
   chunk 15 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.5216

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.102899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.084901 restraints weight = 16241.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.086386 restraints weight = 11510.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.087563 restraints weight = 9016.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.088295 restraints weight = 7528.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.088939 restraints weight = 6601.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.7438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3748  Z= 0.104
  Angle     :  0.565   9.752   5161  Z= 0.287
  Chirality :  0.035   0.189    650
  Planarity :  0.003   0.039    670
  Dihedral  :  3.394  16.141    587
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.57 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 20.74 %
    Favored  : 76.96 %
  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:  2.86 (0.37), residues: 561
  helix:  2.68 (0.25), residues: 439
  sheet:  None (None), residues: 0
  loop : -1.24 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 681 
 TYR   0.010   0.001   TYR A 491 
 PHE   0.022   0.001   PHE A 579 
 TRP   0.030   0.002   TRP A 267 
 HIS   0.003   0.001   HIS A 553 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 3748)
  covalent geometry    : angle       0.56462 ( 5161)
  hydrogen bonds       : bond        0.03034 (  321)
  hydrogen bonds       : angle       3.39648 (  945)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: A  556 ASP cc_start: 0.8052 (p0) cc_final: 0.7614 (m-30)
REVERT: A  558 ILE cc_start: 0.8780 (mm) cc_final: 0.8456 (mm)
REVERT: A  571 TRP cc_start: 0.6411 (m-10) cc_final: 0.6097 (m-10)
REVERT: A  602 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7757 (mm-30)
  outliers start: 5
  outliers final: 5
  residues processed: 49
  average time/residue: 0.0448
  time to fit residues: 2.9782
Evaluate side-chains
  48 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  448 HIS
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  501 HIS
Chi-restraints excluded: chain A residue  530 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 2 optimal weight:   20.0000
   chunk 23 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 614 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.097233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.079693 restraints weight = 15943.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.081037 restraints weight = 11600.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.081985 restraints weight = 9254.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.082690 restraints weight = 7870.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.082894 restraints weight = 6986.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.9155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3748  Z= 0.184
  Angle     :  0.653   9.331   5161  Z= 0.343
  Chirality :  0.038   0.129    650
  Planarity :  0.004   0.049    670
  Dihedral  :  4.194  18.357    587
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.99 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 20.28 %
    Favored  : 76.96 %
  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:  1.93 (0.36), residues: 561
  helix:  1.98 (0.25), residues: 449
  sheet:  None (None), residues: 0
  loop : -1.71 (0.56), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 192 
 TYR   0.013   0.002   TYR A 433 
 PHE   0.027   0.003   PHE A 579 
 TRP   0.024   0.002   TRP A 561 
 HIS   0.008   0.002   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 3748)
  covalent geometry    : angle       0.65325 ( 5161)
  hydrogen bonds       : bond        0.04242 (  321)
  hydrogen bonds       : angle       4.10254 (  945)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 704.96 seconds
wall clock time: 12 minutes 45.96 seconds (765.96 seconds total)