Starting phenix.real_space_refine
on Wed Jul 23 16:14:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8edn_28037/07_2025/8edn_28037.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8edn_28037/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8edn_28037/07_2025/8edn_28037.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8edn_28037/07_2025/8edn_28037.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8edn_28037/07_2025/8edn_28037.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8edn_28037/07_2025/8edn_28037.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 18, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 22, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 7, 'GLU:plan': 30, 'ARG:plan': 14}
          Unresolved non-hydrogen planarities: 485
  Time building chain proxies: 3.07, per 1000 atoms: 0.83
  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: 1.09
  Conformation dependent library (CDL) restraints added in 612.7 milliseconds
  

  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: 0.48
  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: 1.13

  Time building geometry restraints manager: 1.23 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:             1.170
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.800
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.330
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.009   0.001   TRP A 425 
 HIS   0.006   0.001   HIS A 393 
 PHE   0.016   0.001   PHE A 250 
 TYR   0.010   0.001   TYR A 408 
 ARG   0.002   0.001   ARG A 601 

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

*********************** 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  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 ASN cc_start: 0.8178 (t0) cc_final: 0.7626 (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: 0.1722
  time to fit residues: 21.2180
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  : 0.435 
-------------------------------------------------------------------------------
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 48 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0980
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 44 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.109096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.091601 restraints weight = 15158.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.093046 restraints weight = 11244.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.094038 restraints weight = 8934.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6640
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3748  Z= 0.127
  Angle     :  0.554  11.208   5161  Z= 0.287
  Chirality :  0.036   0.155    650
  Planarity :  0.007   0.141    670
  Dihedral  :  4.077  37.525    589
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.28 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.82 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.38), residues: 561
  helix:  2.57 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop : -1.46 (0.64), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 561 
 HIS   0.009   0.002   HIS A 588 
 PHE   0.031   0.003   PHE A 570 
 TYR   0.007   0.001   TYR A 333 
 ARG   0.008   0.001   ARG A 601 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03382 (  321)
  hydrogen bonds       : angle       3.74748 (  945)
  covalent geometry    : bond        0.00253 ( 3748)
  covalent geometry    : angle       0.55371 ( 5161)

*********************** 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
  65 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A  408 TYR cc_start: 0.6545 (t80) cc_final: 0.6243 (t80)
REVERT: A  579 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.6348 (t80)
  outliers start: 6
  outliers final: 3
  residues processed: 64
  average time/residue: 0.1341
  time to fit residues: 11.3381
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  : 0.417 
-------------------------------------------------------------------------------
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 52 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 122 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 = 0.4066 r_free = 0.4066 target = 0.106434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.089036 restraints weight = 15287.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.090557 restraints weight = 11032.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.091471 restraints weight = 8654.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6885
moved from start:          0.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3748  Z= 0.127
  Angle     :  0.551  10.127   5161  Z= 0.289
  Chirality :  0.037   0.149    650
  Planarity :  0.004   0.056    670
  Dihedral  :  3.617  17.442    587
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.03 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 13.82 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.36), residues: 561
  helix:  2.44 (0.24), residues: 443
  sheet:  None (None), residues: 0
  loop : -1.83 (0.56), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 561 
 HIS   0.005   0.001   HIS A 415 
 PHE   0.037   0.003   PHE A 579 
 TYR   0.009   0.002   TYR A 333 
 ARG   0.003   0.001   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03475 (  321)
  hydrogen bonds       : angle       3.60993 (  945)
  covalent geometry    : bond        0.00257 ( 3748)
  covalent geometry    : angle       0.55078 ( 5161)

*********************** 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
  70 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: A  556 ASP cc_start: 0.7645 (p0) cc_final: 0.6881 (m-30)
REVERT: A  598 LYS cc_start: 0.8629 (mttt) cc_final: 0.8169 (mttp)
  outliers start: 12
  outliers final: 7
  residues processed: 68
  average time/residue: 0.1386
  time to fit residues: 12.0048
Evaluate side-chains
  53 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 PHE
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
Chi-restraints excluded: chain A residue  571 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 42 optimal weight:    0.0370
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:   20.0000
   chunk 46 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0770
   chunk 21 optimal weight:    0.0870
   overall best weight:    0.3794

-------------------------------------------------------------------------------
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 = 0.4060 r_free = 0.4060 target = 0.106734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.088451 restraints weight = 15531.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.090010 restraints weight = 11093.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.091017 restraints weight = 8669.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.4896

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= 0.101
  Angle     :  0.538  11.285   5161  Z= 0.270
  Chirality :  0.036   0.133    650
  Planarity :  0.003   0.040    670
  Dihedral  :  3.528  15.497    587
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.92 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 16.59 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.36), residues: 561
  helix:  2.58 (0.24), residues: 444
  sheet:  None (None), residues: 0
  loop : -1.81 (0.57), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 561 
 HIS   0.005   0.001   HIS A 588 
 PHE   0.014   0.002   PHE A 570 
 TYR   0.007   0.001   TYR A 491 
 ARG   0.001   0.000   ARG A 601 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03058 (  321)
  hydrogen bonds       : angle       3.52988 (  945)
  covalent geometry    : bond        0.00199 ( 3748)
  covalent geometry    : angle       0.53752 ( 5161)

*********************** 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
  59 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A  598 LYS cc_start: 0.8662 (mttt) cc_final: 0.8143 (mttp)
REVERT: A  601 ARG cc_start: 0.8296 (ptp90) cc_final: 0.7841 (ptp90)
REVERT: A  602 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7472 (mm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 56
  average time/residue: 0.1516
  time to fit residues: 10.8570
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  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LYS
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 614 ASN
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.098002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.080396 restraints weight = 15954.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.081708 restraints weight = 11755.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.082611 restraints weight = 9379.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.7825

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= 0.214
  Angle     :  0.687   8.937   5161  Z= 0.365
  Chirality :  0.041   0.159    650
  Planarity :  0.005   0.042    670
  Dihedral  :  4.703  20.568    587
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.28 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 18.43 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.35), residues: 561
  helix:  1.61 (0.24), residues: 444
  sheet:  None (None), residues: 0
  loop : -1.95 (0.53), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 599 
 HIS   0.008   0.002   HIS A 501 
 PHE   0.015   0.003   PHE A 610 
 TYR   0.029   0.003   TYR A 333 
 ARG   0.004   0.001   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04610 (  321)
  hydrogen bonds       : angle       4.44127 (  945)
  covalent geometry    : bond        0.00446 ( 3748)
  covalent geometry    : angle       0.68658 ( 5161)

*********************** 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
  59 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  556 ASP cc_start: 0.7936 (p0) cc_final: 0.7220 (m-30)
REVERT: A  598 LYS cc_start: 0.8677 (mttt) cc_final: 0.8321 (mttp)
  outliers start: 12
  outliers final: 8
  residues processed: 56
  average time/residue: 0.1357
  time to fit residues: 9.8361
Evaluate side-chains
  48 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LYS
Chi-restraints excluded: chain A residue  300 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 22 optimal weight:    0.0870
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 54 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 393 HIS
A 614 ASN
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.100135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.082424 restraints weight = 15941.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.083709 restraints weight = 11650.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.084761 restraints weight = 9366.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.7986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   3748  Z= 0.117
  Angle     :  0.596  11.078   5161  Z= 0.301
  Chirality :  0.036   0.145    650
  Planarity :  0.004   0.041    670
  Dihedral  :  3.952  16.337    587
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.28 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 20.28 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.36), residues: 561
  helix:  2.21 (0.25), residues: 443
  sheet:  None (None), residues: 0
  loop : -1.84 (0.55), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 561 
 HIS   0.005   0.001   HIS A 588 
 PHE   0.023   0.002   PHE A 579 
 TYR   0.009   0.001   TYR A 408 
 ARG   0.002   0.000   ARG A 607 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03455 (  321)
  hydrogen bonds       : angle       3.72723 (  945)
  covalent geometry    : bond        0.00239 ( 3748)
  covalent geometry    : angle       0.59623 ( 5161)

*********************** 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: 9
    poor density    : 42
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A  556 ASP cc_start: 0.7964 (p0) cc_final: 0.7049 (m-30)
REVERT: A  598 LYS cc_start: 0.8542 (mttt) cc_final: 0.8229 (mttp)
  outliers start: 9
  outliers final: 7
  residues processed: 47
  average time/residue: 0.1394
  time to fit residues: 8.5774
Evaluate side-chains
  48 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LYS
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  551 VAL
Chi-restraints excluded: chain A residue  600 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 25 optimal weight:    0.0270
   chunk 31 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 43 optimal weight:    0.1980
   chunk 22 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.4638

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.100829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.083285 restraints weight = 15523.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.084749 restraints weight = 11120.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.085756 restraints weight = 8752.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.8166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3748  Z= 0.105
  Angle     :  0.602  13.422   5161  Z= 0.299
  Chirality :  0.036   0.151    650
  Planarity :  0.003   0.040    670
  Dihedral  :  3.677  15.252    587
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.28 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 22.12 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.37), residues: 561
  helix:  2.32 (0.25), residues: 445
  sheet:  None (None), residues: 0
  loop : -1.81 (0.56), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 571 
 HIS   0.004   0.001   HIS A 588 
 PHE   0.018   0.001   PHE A 579 
 TYR   0.011   0.001   TYR A 408 
 ARG   0.002   0.000   ARG A 607 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03244 (  321)
  hydrogen bonds       : angle       3.52493 (  945)
  covalent geometry    : bond        0.00214 ( 3748)
  covalent geometry    : angle       0.60201 ( 5161)

*********************** 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
  52 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 ASN cc_start: 0.8458 (m110) cc_final: 0.8057 (m-40)
REVERT: A  556 ASP cc_start: 0.8065 (p0) cc_final: 0.7416 (m-30)
REVERT: A  598 LYS cc_start: 0.8645 (mttt) cc_final: 0.8281 (mttp)
  outliers start: 8
  outliers final: 6
  residues processed: 49
  average time/residue: 0.1483
  time to fit residues: 9.4316
Evaluate side-chains
  47 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LYS
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  600 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0970
   chunk 41 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.100641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.083004 restraints weight = 15848.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.084351 restraints weight = 11416.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.085503 restraints weight = 9069.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.8510

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= 0.105
  Angle     :  0.566   9.301   5161  Z= 0.283
  Chirality :  0.035   0.166    650
  Planarity :  0.003   0.041    670
  Dihedral  :  3.562  14.941    587
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.46 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.66 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.37), residues: 561
  helix:  2.48 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -1.69 (0.57), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 561 
 HIS   0.004   0.001   HIS A 588 
 PHE   0.033   0.002   PHE A 570 
 TYR   0.006   0.001   TYR A 227 
 ARG   0.001   0.000   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03131 (  321)
  hydrogen bonds       : angle       3.47586 (  945)
  covalent geometry    : bond        0.00223 ( 3748)
  covalent geometry    : angle       0.56565 ( 5161)

*********************** 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
  54 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  553 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.6569 (t-90)
REVERT: A  556 ASP cc_start: 0.8121 (p0) cc_final: 0.7421 (m-30)
REVERT: A  598 LYS cc_start: 0.8600 (mttt) cc_final: 0.8286 (mttp)
  outliers start: 8
  outliers final: 5
  residues processed: 51
  average time/residue: 0.1505
  time to fit residues: 9.8142
Evaluate side-chains
  49 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LYS
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  553 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 56 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9980
   chunk 42 optimal weight:    0.2980
   chunk 0 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 8 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0170
   chunk 13 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.0220

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.098535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.081516 restraints weight = 15780.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.082823 restraints weight = 11536.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.083824 restraints weight = 9216.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.8939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3748  Z= 0.119
  Angle     :  0.570   8.786   5161  Z= 0.293
  Chirality :  0.036   0.167    650
  Planarity :  0.004   0.046    670
  Dihedral  :  3.636  14.839    587
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.63 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.04 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.37), residues: 561
  helix:  2.48 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -1.66 (0.57), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 561 
 HIS   0.004   0.001   HIS A 501 
 PHE   0.038   0.002   PHE A 570 
 TYR   0.011   0.001   TYR A 227 
 ARG   0.004   0.001   ARG A 607 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03307 (  321)
  hydrogen bonds       : angle       3.58949 (  945)
  covalent geometry    : bond        0.00252 ( 3748)
  covalent geometry    : angle       0.56964 ( 5161)

*********************** 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
  49 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.409 
Fit side-chains
REVERT: A  553 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.6568 (t-90)
REVERT: A  556 ASP cc_start: 0.8131 (p0) cc_final: 0.7417 (m-30)
REVERT: A  571 TRP cc_start: 0.7251 (m100) cc_final: 0.6771 (m100)
REVERT: A  598 LYS cc_start: 0.8575 (mttt) cc_final: 0.8305 (mttp)
  outliers start: 6
  outliers final: 5
  residues processed: 48
  average time/residue: 0.1451
  time to fit residues: 9.2315
Evaluate side-chains
  47 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LYS
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  553 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 56 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 2 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.3844 r_free = 0.3844 target = 0.092768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.076445 restraints weight = 16260.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.077886 restraints weight = 11189.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.078868 restraints weight = 8617.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          1.0334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3748  Z= 0.204
  Angle     :  0.695  11.666   5161  Z= 0.369
  Chirality :  0.039   0.186    650
  Planarity :  0.004   0.029    670
  Dihedral  :  4.504  17.946    587
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.70 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 23.04 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.36), residues: 561
  helix:  1.73 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -1.72 (0.57), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 561 
 HIS   0.009   0.002   HIS A 175 
 PHE   0.030   0.003   PHE A 570 
 TYR   0.017   0.003   TYR A 433 
 ARG   0.004   0.001   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04755 (  321)
  hydrogen bonds       : angle       4.38003 (  945)
  covalent geometry    : bond        0.00431 ( 3748)
  covalent geometry    : angle       0.69523 ( 5161)

********************** 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
  49 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.434 
Fit side-chains
REVERT: A  556 ASP cc_start: 0.8265 (p0) cc_final: 0.7499 (m-30)
REVERT: A  598 LYS cc_start: 0.8855 (mttt) cc_final: 0.8483 (mttp)
REVERT: A  693 MET cc_start: 0.5755 (tpt) cc_final: 0.5487 (tpp)
  outliers start: 8
  outliers final: 8
  residues processed: 47
  average time/residue: 0.1504
  time to fit residues: 9.1603
Evaluate side-chains
  44 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LYS
Chi-restraints excluded: chain A residue  300 LEU
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  553 HIS
Chi-restraints excluded: chain A residue  600 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 5 optimal weight:    0.2980
   chunk 7 optimal weight:    9.9990
   chunk 56 optimal weight:   20.0000
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.095123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.078374 restraints weight = 15988.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.079917 restraints weight = 10877.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.081047 restraints weight = 8346.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          1.0371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3748  Z= 0.121
  Angle     :  0.623  11.491   5161  Z= 0.324
  Chirality :  0.036   0.160    650
  Planarity :  0.004   0.033    670
  Dihedral  :  3.957  17.905    587
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.28 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.50 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.37), residues: 561
  helix:  2.16 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -1.70 (0.60), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 561 
 HIS   0.005   0.001   HIS A 175 
 PHE   0.028   0.002   PHE A 570 
 TYR   0.009   0.001   TYR A 227 
 ARG   0.012   0.001   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03665 (  321)
  hydrogen bonds       : angle       3.80984 (  945)
  covalent geometry    : bond        0.00252 ( 3748)
  covalent geometry    : angle       0.62286 ( 5161)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1509.20 seconds
wall clock time: 26 minutes 42.61 seconds (1602.61 seconds total)