Starting phenix.real_space_refine
on Tue Mar 11 18:27:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b7q_15899/03_2025/8b7q_15899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b7q_15899/03_2025/8b7q_15899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b7q_15899/03_2025/8b7q_15899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b7q_15899/03_2025/8b7q_15899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b7q_15899/03_2025/8b7q_15899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b7q_15899/03_2025/8b7q_15899.cif"
  }
  resolution = 4.02
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3495 atoms to isotropic.
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      18      5.16       5
     C    2236      2.51       5
     N     594      2.21       5
     O     663      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3511
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1064
          Classifications: {'peptide': 138}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 131}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1637
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 190}
    Chain: "F"
      Number of atoms: 796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 796
          Classifications: {'peptide': 97}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.03, per 1000 atoms: 1.15
  Number of scatterers: 3511
  At special positions: 0
  Unit cell: (79.584, 98.651, 88.703, 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      18     16.00
     O     663      8.00
     N     594      7.00
     C    2236      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 496 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 350 " - pdb=" SG  CYS F 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 411 " - pdb=" SG  CYS F 416 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG F 901 " - " ASN F 345 "
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 470.8 milliseconds
  

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  850

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 8 sheets defined
      25.9% alpha, 32.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 45
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.870A  pdb=" N   GLN A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   SER A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 45 through 50'
    Processing helix  chain 'A' and resid 71 through 89
      removed outlier: 3.647A  pdb=" N   SER A  88 " --> pdb=" O   GLN A  84 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A  89 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 113
    Processing helix  chain 'A' and resid 130 through 138
    Processing helix  chain 'A' and resid 138 through 162
      removed outlier: 4.117A  pdb=" N   ASP A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.963A  pdb=" N   VAL B 533 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 375 through 377
      No H-bonds generated for 'chain 'F' and resid 375 through 377'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 432 through 436
      removed outlier: 3.536A  pdb=" N   TRP B 447 " --> pdb=" O   TYR B 494 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.491A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.491A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 539 through 546
      removed outlier: 5.035A  pdb=" N   ASN B 540 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLU B 557 " --> pdb=" O   ASN B 540 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 582 through 586
    Processing sheet with id=AA6, first strand: chain 'F' and resid 331 through 334
    Processing sheet with id=AA7, first strand: chain 'F' and resid 331 through 334
      removed outlier: 3.552A  pdb=" N   ALA F 346 " --> pdb=" O   PHE F 391 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 337 through 340
      removed outlier: 7.582A  pdb=" N   HIS F 417 " --> pdb=" O   ASN F 412 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   ASN F 412 " --> pdb=" O   HIS F 417 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ARG F 419 " --> pdb=" O   CYS F 410 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   CYS F 410 " --> pdb=" O   ARG F 419 " (cutoff:3.500A)

    175 hydrogen bonds defined for protein.
    474 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: 1.03

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1124
        1.34 -     1.46: 812
        1.46 -     1.58: 1630
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 3588
  Sorted by residual:
  bond pdb=" C1  NAG F 901 "
       pdb=" O5  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.75e+00
  bond pdb=" C5  NAG F 901 "
       pdb=" O5  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  bond pdb=" C3  NAG F 901 "
       pdb=" O3  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.76e-01
  bond pdb=" C   TRP B 447 "
       pdb=" N   SER B 448 "
    ideal  model  delta    sigma   weight residual
    1.332  1.347 -0.015 1.92e-02 2.71e+03 6.28e-01
  bond pdb=" N   SER A 114 "
       pdb=" CA  SER A 114 "
    ideal  model  delta    sigma   weight residual
    1.463  1.455  0.008 1.08e-02 8.57e+03 5.33e-01
  ... (remaining 3583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 4692
        1.40 -     2.81: 165
        2.81 -     4.21: 26
        4.21 -     5.62: 1
        5.62 -     7.02: 1
  Bond angle restraints: 4885
  Sorted by residual:
  angle pdb=" C   ILE A  63 "
        pdb=" N   PRO A  64 "
        pdb=" CA  PRO A  64 "
      ideal   model   delta    sigma   weight residual
     119.84  122.92   -3.08 1.25e+00 6.40e-01 6.05e+00
  angle pdb=" C   PHE A 113 "
        pdb=" N   SER A 114 "
        pdb=" CA  SER A 114 "
      ideal   model   delta    sigma   weight residual
     120.89  124.35   -3.46 1.50e+00 4.44e-01 5.32e+00
  angle pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
        pdb=" C   SER A  46 "
      ideal   model   delta    sigma   weight residual
     111.37  115.17   -3.80 1.65e+00 3.67e-01 5.30e+00
  angle pdb=" C   ILE A  45 "
        pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
      ideal   model   delta    sigma   weight residual
     120.82  124.00   -3.18 1.50e+00 4.44e-01 4.50e+00
  angle pdb=" N   LEU B 503 "
        pdb=" CA  LEU B 503 "
        pdb=" C   LEU B 503 "
      ideal   model   delta    sigma   weight residual
     111.33  113.75   -2.42 1.21e+00 6.83e-01 4.01e+00
  ... (remaining 4880 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 2086
       15.92 -    31.83: 94
       31.83 -    47.75: 22
       47.75 -    63.66: 4
       63.66 -    79.58: 2
  Dihedral angle restraints: 2208
    sinusoidal: 903
      harmonic: 1305
  Sorted by residual:
  dihedral pdb=" CB  CYS F 350 "
           pdb=" SG  CYS F 350 "
           pdb=" SG  CYS F 410 "
           pdb=" CB  CYS F 410 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.39   29.61     1      1.00e+01 1.00e-02 1.25e+01
  dihedral pdb=" N   LEU A 161 "
           pdb=" CA  LEU A 161 "
           pdb=" CB  LEU A 161 "
           pdb=" CG  LEU A 161 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.82  -58.18     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" N   PHE F 334 "
           pdb=" CA  PHE F 334 "
           pdb=" CB  PHE F 334 "
           pdb=" CG  PHE F 334 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.09   51.09     3      1.50e+01 4.44e-03 8.98e+00
  ... (remaining 2205 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 349
       0.031 -    0.062: 154
       0.062 -    0.092: 33
       0.092 -    0.123: 31
       0.123 -    0.154: 5
  Chirality restraints: 572
  Sorted by residual:
  chirality pdb=" CA  ILE F 351 "
            pdb=" N   ILE F 351 "
            pdb=" C   ILE F 351 "
            pdb=" CB  ILE F 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.91e-01
  chirality pdb=" CA  PRO A  64 "
            pdb=" N   PRO A  64 "
            pdb=" C   PRO A  64 "
            pdb=" CB  PRO A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" CA  ILE F 374 "
            pdb=" N   ILE F 374 "
            pdb=" C   ILE F 374 "
            pdb=" CB  ILE F 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 569 not shown)

  Planarity restraints: 616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 155 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   GLN A 155 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLN A 155 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP A 156 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 448 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO B 449 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 449 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 449 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 148 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.63e+00
        pdb=" C   SER A 148 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   SER A 148 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ARG A 149 "    0.007 2.00e-02 2.50e+03
  ... (remaining 613 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 532
        2.77 -     3.30: 3250
        3.30 -     3.83: 5553
        3.83 -     4.37: 6419
        4.37 -     4.90: 11088
  Nonbonded interactions: 26842
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 141 "
            pdb=" OH  TYR F 409 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   PRO A  64 "
            pdb=" OH  TYR A  82 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OD2 ASP A  30 "
            pdb=" OH  TYR B 470 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" NH2 ARG B 571 "
            pdb=" OE1 GLN B 608 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" NH2 ARG F 400 "
            pdb=" O   TYR F 405 "
     model   vdw
     2.378 3.120
  ... (remaining 26837 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             4.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.640
  Find NCS groups from input model:        0.030
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3588  Z= 0.173
  Angle     :  0.599   7.021   4885  Z= 0.335
  Chirality :  0.043   0.154    572
  Planarity :  0.004   0.035    615
  Dihedral  :  9.873  79.577   1340
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  3.93 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  6.13 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  0.29 (0.38), residues: 433
  helix:  0.92 (0.47), residues: 97
  sheet:  0.83 (0.39), residues: 134
  loop : -0.57 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 367 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.010   0.001   PHE B 493 
 TYR   0.009   0.001   TYR F 424 
 ARG   0.002   0.000   ARG B 467 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ILE cc_start: 0.7042 (mt) cc_final: 0.6621 (mm)
REVERT: A   63 ILE cc_start: 0.8987 (mt) cc_final: 0.8664 (tt)
REVERT: A   93 ASN cc_start: 0.7569 (m-40) cc_final: 0.7287 (m-40)
REVERT: B  436 THR cc_start: 0.9047 (m) cc_final: 0.8331 (m)
REVERT: B  540 ASN cc_start: 0.8477 (t0) cc_final: 0.8226 (t0)
REVERT: B  565 ASN cc_start: 0.8276 (m-40) cc_final: 0.7795 (p0)
REVERT: B  572 TYR cc_start: 0.8019 (p90) cc_final: 0.7631 (p90)
REVERT: B  585 GLU cc_start: 0.8506 (mp0) cc_final: 0.8236 (pm20)
REVERT: B  609 VAL cc_start: 0.9427 (t) cc_final: 0.9200 (m)
REVERT: B  612 ARG cc_start: 0.8665 (ttt180) cc_final: 0.7832 (ttt-90)
REVERT: F  365 VAL cc_start: 0.8987 (m) cc_final: 0.8090 (p)
REVERT: F  388 LYS cc_start: 0.8796 (tttt) cc_final: 0.8555 (tttp)
REVERT: F  393 ASN cc_start: 0.7524 (t0) cc_final: 0.7077 (t0)
  outliers start: 12
  outliers final: 2
  residues processed: 155
  average time/residue: 0.1705
  time to fit residues: 31.6744
Evaluate side-chains
  97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.113202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.092825 restraints weight = 8006.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.095586 restraints weight = 4681.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.097548 restraints weight = 3232.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3588  Z= 0.217
  Angle     :  0.631  10.846   4885  Z= 0.322
  Chirality :  0.046   0.266    572
  Planarity :  0.004   0.042    615
  Dihedral  :  4.335  16.588    496
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  1.72 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  1.14 (0.40), residues: 433
  helix:  2.30 (0.50), residues: 103
  sheet:  0.55 (0.38), residues: 135
  loop :  0.16 (0.48), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 620 
 HIS   0.003   0.001   HIS F 418 
 PHE   0.012   0.002   PHE A 113 
 TYR   0.020   0.002   TYR A  82 
 ARG   0.004   0.000   ARG F 419 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8512 (ttpt) cc_final: 0.8099 (ttpt)
REVERT: A   93 ASN cc_start: 0.7650 (m-40) cc_final: 0.7430 (m-40)
REVERT: B  572 TYR cc_start: 0.8111 (p90) cc_final: 0.7727 (p90)
REVERT: B  609 VAL cc_start: 0.9487 (t) cc_final: 0.9282 (m)
REVERT: B  612 ARG cc_start: 0.8864 (ttt180) cc_final: 0.8333 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8683 (pt) cc_final: 0.8462 (mm)
REVERT: F  393 ASN cc_start: 0.7585 (t0) cc_final: 0.6997 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1491
  time to fit residues: 20.7646
Evaluate side-chains
  89 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 GLN
B 461 GLN
B 499 GLN
F 354 ASN
F 369 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.112584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.091818 restraints weight = 8070.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.094476 restraints weight = 4879.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.096301 restraints weight = 3429.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3588  Z= 0.213
  Angle     :  0.613  14.128   4885  Z= 0.314
  Chirality :  0.046   0.236    572
  Planarity :  0.004   0.031    615
  Dihedral  :  4.373  25.322    496
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.45 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  1.39 (0.41), residues: 433
  helix:  2.69 (0.50), residues: 102
  sheet:  0.67 (0.42), residues: 123
  loop :  0.27 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.011   0.001   PHE F 348 
 TYR   0.016   0.001   TYR F 352 
 ARG   0.002   0.000   ARG F 419 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.461 
Fit side-chains
REVERT: A   74 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8282 (ttpt)
REVERT: B  429 ASN cc_start: 0.8926 (t0) cc_final: 0.8622 (t0)
REVERT: B  609 VAL cc_start: 0.9428 (t) cc_final: 0.9191 (m)
REVERT: B  612 ARG cc_start: 0.8871 (ttt180) cc_final: 0.8465 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8625 (pt) cc_final: 0.8343 (mm)
REVERT: F  393 ASN cc_start: 0.7496 (t0) cc_final: 0.6929 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1567
  time to fit residues: 21.0081
Evaluate side-chains
  84 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.111270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.090798 restraints weight = 8043.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.093377 restraints weight = 4955.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.095164 restraints weight = 3538.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.4391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3588  Z= 0.215
  Angle     :  0.609  12.482   4885  Z= 0.310
  Chirality :  0.045   0.187    572
  Planarity :  0.004   0.030    615
  Dihedral  :  4.542  31.216    496
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.42 (0.41), residues: 433
  helix:  2.73 (0.50), residues: 102
  sheet:  0.80 (0.42), residues: 128
  loop :  0.17 (0.47), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 465 
 PHE   0.010   0.001   PHE F 348 
 TYR   0.012   0.001   TYR F 424 
 ARG   0.002   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A   69 ILE cc_start: 0.7228 (tp) cc_final: 0.6974 (tp)
REVERT: A   74 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8304 (ttpt)
REVERT: B  429 ASN cc_start: 0.8891 (t0) cc_final: 0.8619 (t0)
REVERT: B  542 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8252 (mmtm)
REVERT: B  572 TYR cc_start: 0.8012 (p90) cc_final: 0.7634 (p90)
REVERT: B  612 ARG cc_start: 0.8881 (ttt180) cc_final: 0.8348 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8672 (pt) cc_final: 0.8299 (mm)
REVERT: F  393 ASN cc_start: 0.7473 (t0) cc_final: 0.7068 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1513
  time to fit residues: 18.5499
Evaluate side-chains
  82 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
F 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.111192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.090871 restraints weight = 8304.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.093475 restraints weight = 5065.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.095325 restraints weight = 3567.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.4634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3588  Z= 0.196
  Angle     :  0.586  11.023   4885  Z= 0.299
  Chirality :  0.044   0.181    572
  Planarity :  0.004   0.029    615
  Dihedral  :  4.498  30.637    496
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.47 (0.41), residues: 433
  helix:  2.94 (0.51), residues: 102
  sheet:  0.80 (0.42), residues: 128
  loop :  0.12 (0.47), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 584 
 PHE   0.008   0.001   PHE F 348 
 TYR   0.011   0.001   TYR F 424 
 ARG   0.004   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8189 (ptm160)
REVERT: A   69 ILE cc_start: 0.7177 (tp) cc_final: 0.6904 (tp)
REVERT: A   74 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8301 (ttpt)
REVERT: B  429 ASN cc_start: 0.8870 (t0) cc_final: 0.8611 (t0)
REVERT: B  453 GLN cc_start: 0.8716 (pt0) cc_final: 0.8308 (pm20)
REVERT: B  542 LYS cc_start: 0.8549 (mmmm) cc_final: 0.8275 (mmtm)
REVERT: B  572 TYR cc_start: 0.7993 (p90) cc_final: 0.7593 (p90)
REVERT: B  612 ARG cc_start: 0.8864 (ttt180) cc_final: 0.8422 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8639 (pt) cc_final: 0.8352 (mm)
REVERT: F  393 ASN cc_start: 0.7417 (t0) cc_final: 0.6929 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1559
  time to fit residues: 19.0577
Evaluate side-chains
  82 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.109516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.088480 restraints weight = 8384.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.091057 restraints weight = 5165.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.092889 restraints weight = 3676.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.4905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3588  Z= 0.242
  Angle     :  0.609  10.653   4885  Z= 0.312
  Chirality :  0.046   0.181    572
  Planarity :  0.004   0.026    615
  Dihedral  :  4.623  30.125    496
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.27 (0.41), residues: 433
  helix:  3.03 (0.50), residues: 96
  sheet:  0.72 (0.42), residues: 128
  loop : -0.08 (0.46), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 465 
 PHE   0.012   0.001   PHE F 334 
 TYR   0.013   0.001   TYR F 424 
 ARG   0.003   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8184 (ptm160)
REVERT: A   69 ILE cc_start: 0.7152 (tp) cc_final: 0.6753 (tp)
REVERT: A   74 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8310 (ttpt)
REVERT: B  429 ASN cc_start: 0.8846 (t0) cc_final: 0.8600 (t0)
REVERT: B  453 GLN cc_start: 0.8734 (pt0) cc_final: 0.8228 (pm20)
REVERT: B  542 LYS cc_start: 0.8590 (mmmm) cc_final: 0.8324 (mmtm)
REVERT: B  612 ARG cc_start: 0.8914 (ttt180) cc_final: 0.8545 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7480 (t0) cc_final: 0.6900 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1598
  time to fit residues: 19.5906
Evaluate side-chains
  80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 13 optimal weight:    0.1980
   chunk 14 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 453 GLN
B 461 GLN
B 499 GLN
** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.110336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.089964 restraints weight = 8079.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.092639 restraints weight = 4908.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.094486 restraints weight = 3454.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.5154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3588  Z= 0.188
  Angle     :  0.594   9.475   4885  Z= 0.302
  Chirality :  0.045   0.163    572
  Planarity :  0.003   0.027    615
  Dihedral  :  4.577  33.357    496
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.22 (0.41), residues: 433
  helix:  2.40 (0.51), residues: 108
  sheet:  0.75 (0.43), residues: 130
  loop :  0.00 (0.47), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.008   0.001   PHE F 334 
 TYR   0.010   0.001   TYR F 424 
 ARG   0.002   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8185 (ptm160)
REVERT: A   69 ILE cc_start: 0.7157 (tp) cc_final: 0.6698 (tp)
REVERT: A   74 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8277 (ttpt)
REVERT: B  429 ASN cc_start: 0.8827 (t0) cc_final: 0.8586 (t0)
REVERT: B  453 GLN cc_start: 0.8635 (pt0) cc_final: 0.8168 (pm20)
REVERT: B  542 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8314 (mmtm)
REVERT: B  572 TYR cc_start: 0.8036 (p90) cc_final: 0.7640 (p90)
REVERT: B  612 ARG cc_start: 0.8880 (ttt180) cc_final: 0.8559 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7403 (t0) cc_final: 0.6838 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1809
  time to fit residues: 22.4187
Evaluate side-chains
  81 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0670
   chunk 26 optimal weight:    0.4980
   chunk 18 optimal weight:    0.0030
   chunk 33 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.3328

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.113139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.092573 restraints weight = 8171.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.095296 restraints weight = 4825.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.097109 restraints weight = 3351.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.5257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3588  Z= 0.155
  Angle     :  0.572   8.519   4885  Z= 0.292
  Chirality :  0.045   0.166    572
  Planarity :  0.003   0.029    615
  Dihedral  :  4.487  37.447    496
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.29 (0.41), residues: 433
  helix:  2.47 (0.52), residues: 108
  sheet:  0.93 (0.44), residues: 127
  loop : -0.05 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.002   0.001   HIS B 465 
 PHE   0.008   0.001   PHE F 334 
 TYR   0.007   0.001   TYR B 494 
 ARG   0.001   0.000   ARG F 385 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8184 (ptm160)
REVERT: B  429 ASN cc_start: 0.8813 (t0) cc_final: 0.8596 (t0)
REVERT: B  542 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8311 (mmtm)
REVERT: B  610 ARG cc_start: 0.7162 (ptt180) cc_final: 0.6810 (ttp-170)
REVERT: B  612 ARG cc_start: 0.8887 (ttt180) cc_final: 0.8405 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7489 (t0) cc_final: 0.6896 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1561
  time to fit residues: 19.5022
Evaluate side-chains
  81 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0170
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8024

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN
B 499 GLN
** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.110351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.090544 restraints weight = 8092.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.092970 restraints weight = 5031.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.094614 restraints weight = 3607.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.5339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3588  Z= 0.236
  Angle     :  0.614   8.171   4885  Z= 0.315
  Chirality :  0.046   0.230    572
  Planarity :  0.004   0.029    615
  Dihedral  :  4.645  35.818    496
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.26 (0.41), residues: 433
  helix:  2.63 (0.51), residues: 102
  sheet:  0.73 (0.42), residues: 141
  loop : -0.01 (0.47), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 465 
 PHE   0.013   0.001   PHE F 334 
 TYR   0.017   0.001   TYR A  82 
 ARG   0.001   0.000   ARG B 613 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8233 (ptm160)
REVERT: A   74 LYS cc_start: 0.8374 (ttpt) cc_final: 0.7891 (ttpt)
REVERT: B  429 ASN cc_start: 0.8821 (t0) cc_final: 0.8419 (t0)
REVERT: B  453 GLN cc_start: 0.8730 (pt0) cc_final: 0.8159 (pm20)
REVERT: B  612 ARG cc_start: 0.8944 (ttt180) cc_final: 0.8620 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7400 (t0) cc_final: 0.6535 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1722
  time to fit residues: 20.5855
Evaluate side-chains
  79 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0970
   chunk 14 optimal weight:    0.9980
   chunk 23 optimal weight:    0.2980
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0170
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.3616

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 453 GLN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.112531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.092450 restraints weight = 8029.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.095020 restraints weight = 4931.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.096763 restraints weight = 3493.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.5558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3588  Z= 0.163
  Angle     :  0.588   6.921   4885  Z= 0.298
  Chirality :  0.045   0.263    572
  Planarity :  0.004   0.030    615
  Dihedral  :  4.446  34.440    496
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.27 (0.41), residues: 433
  helix:  2.46 (0.51), residues: 108
  sheet:  0.90 (0.45), residues: 129
  loop : -0.07 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 478 
 PHE   0.007   0.001   PHE F 348 
 TYR   0.008   0.001   TYR B 439 
 ARG   0.002   0.000   ARG B 463 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8511 (ttp80) cc_final: 0.8252 (ptm160)
REVERT: A   74 LYS cc_start: 0.8340 (ttpt) cc_final: 0.7922 (ttpt)
REVERT: B  429 ASN cc_start: 0.8801 (t0) cc_final: 0.8594 (t0)
REVERT: B  453 GLN cc_start: 0.8755 (pt0) cc_final: 0.8221 (pm20)
REVERT: B  478 HIS cc_start: 0.6862 (m-70) cc_final: 0.6441 (m170)
REVERT: B  612 ARG cc_start: 0.8889 (ttt180) cc_final: 0.8432 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7506 (t0) cc_final: 0.6735 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1602
  time to fit residues: 19.3976
Evaluate side-chains
  80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 4 optimal weight:    0.2980
   chunk 37 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0040
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN
B 465 HIS
B 478 HIS
B 499 GLN
F 369 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.111620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.091289 restraints weight = 8192.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.093775 restraints weight = 5110.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.095543 restraints weight = 3665.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.5567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3588  Z= 0.196
  Angle     :  0.597   6.735   4885  Z= 0.307
  Chirality :  0.045   0.229    572
  Planarity :  0.004   0.042    615
  Dihedral  :  4.491  33.353    496
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.24 (0.41), residues: 433
  helix:  2.47 (0.51), residues: 108
  sheet:  0.64 (0.44), residues: 138
  loop :  0.06 (0.47), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 366 
 HIS   0.006   0.001   HIS B 478 
 PHE   0.008   0.001   PHE F 348 
 TYR   0.011   0.001   TYR A  82 
 ARG   0.007   0.000   ARG F 398 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1927.38 seconds
wall clock time: 33 minutes 52.88 seconds (2032.88 seconds total)