Starting phenix.real_space_refine
on Fri Feb 14 10:02:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k8d_22728/02_2025/7k8d_22728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k8d_22728/02_2025/7k8d_22728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k8d_22728/02_2025/7k8d_22728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k8d_22728/02_2025/7k8d_22728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k8d_22728/02_2025/7k8d_22728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k8d_22728/02_2025/7k8d_22728.cif"
  }
  resolution = 4.33
  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
-------------------------------------------------------------------------------
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=   0.134
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 5528 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      28      5.16       5
     C    3577      2.51       5
     N     918      2.21       5
     O    1006      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5529
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 725, 5529
          Classifications: {'peptide': 725}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 36, 'TRANS': 688}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.45, per 1000 atoms: 0.62
  Number of scatterers: 5529
  At special positions: 0
  Unit cell: (76.96, 74.88, 111.28, 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      28     16.00
     O    1006      8.00
     N     918      7.00
     C    3577      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: 1.51
  Conformation dependent library (CDL) restraints added in 864.0 milliseconds
  

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1326

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 2 sheets defined
      75.6% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 12
      removed outlier: 4.156A  pdb=" N   TYR A  10 " --> pdb=" O   GLY A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 34
      removed outlier: 3.502A  pdb=" N   LEU A  25 " --> pdb=" O   VAL A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 62
      removed outlier: 3.886A  pdb=" N   VAL A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ALA A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 101
    Processing helix  chain 'A' and resid 110 through 114
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 143 through 160
      Proline residue:  A 156  - end of helix
    Processing helix  chain 'A' and resid 161 through 165
    Processing helix  chain 'A' and resid 170 through 205
      removed outlier: 3.883A  pdb=" N   ILE A 194 " --> pdb=" O   GLU A 190 " (cutoff:3.500A)
      Proline residue:  A 195  - end of helix
    Processing helix  chain 'A' and resid 207 through 233
      removed outlier: 3.667A  pdb=" N   ALA A 211 " --> pdb=" O   THR A 207 " (cutoff:3.500A)
      Proline residue:  A 214  - end of helix
    Processing helix  chain 'A' and resid 241 through 272
      removed outlier: 3.705A  pdb=" N   VAL A 245 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY A 272 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 307
      removed outlier: 3.690A  pdb=" N   THR A 289 " --> pdb=" O   THR A 285 " (cutoff:3.500A)
      Proline residue:  A 303  - end of helix
    Processing helix  chain 'A' and resid 310 through 332
    Processing helix  chain 'A' and resid 332 through 342
      removed outlier: 3.697A  pdb=" N   LEU A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 347
      removed outlier: 3.805A  pdb=" N   ALA A 347 " --> pdb=" O   ARG A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 400
    Processing helix  chain 'A' and resid 401 through 416
      Proline residue:  A 407  - end of helix
      removed outlier: 3.738A  pdb=" N   VAL A 413 " --> pdb=" O   LEU A 409 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LEU A 414 " --> pdb=" O   VAL A 410 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU A 415 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ILE A 416 " --> pdb=" O   MET A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 422
    Processing helix  chain 'A' and resid 428 through 432
      removed outlier: 3.726A  pdb=" N   LEU A 432 " --> pdb=" O   GLU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 449
    Processing helix  chain 'A' and resid 470 through 483
    Processing helix  chain 'A' and resid 493 through 497
    Processing helix  chain 'A' and resid 524 through 535
      removed outlier: 4.584A  pdb=" N   LYS A 528 " --> pdb=" O   ASN A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 583
      Proline residue:  A 565  - end of helix
    Processing helix  chain 'A' and resid 586 through 612
      removed outlier: 4.035A  pdb=" N   ILE A 590 " --> pdb=" O   VAL A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 621
      removed outlier: 3.647A  pdb=" N   MET A 620 " --> pdb=" O   GLY A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 660
      removed outlier: 3.557A  pdb=" N   ILE A 632 " --> pdb=" O   MET A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 675
    Processing helix  chain 'A' and resid 675 through 695
    Processing helix  chain 'A' and resid 698 through 718
    Processing helix  chain 'A' and resid 718 through 732
      Proline residue:  A 725  - end of helix
    Processing helix  chain 'A' and resid 733 through 737
    Processing helix  chain 'A' and resid 739 through 748
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 73
      removed outlier: 3.617A  pdb=" N   LEU A  73 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   THR A 133 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 513 through 518

    396 hydrogen bonds defined for protein.
    1149 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: 1.63

  Time building geometry restraints manager: 1.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1324
        1.33 -     1.45: 1034
        1.45 -     1.57: 3227
        1.57 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 5639
  Sorted by residual:
  bond pdb=" C   ILE A 417 "
       pdb=" O   ILE A 417 "
    ideal  model  delta    sigma   weight residual
    1.242  1.224  0.018 8.60e-03 1.35e+04 4.33e+00
  bond pdb=" N   ALA A 526 "
       pdb=" CA  ALA A 526 "
    ideal  model  delta    sigma   weight residual
    1.459  1.435  0.024 1.19e-02 7.06e+03 4.23e+00
  bond pdb=" C   VAL A 411 "
       pdb=" O   VAL A 411 "
    ideal  model  delta    sigma   weight residual
    1.237  1.214  0.023 1.23e-02 6.61e+03 3.57e+00
  bond pdb=" CA  ASP A 525 "
       pdb=" C   ASP A 525 "
    ideal  model  delta    sigma   weight residual
    1.523  1.497  0.026 1.41e-02 5.03e+03 3.39e+00
  bond pdb=" CB  MET A 461 "
       pdb=" CG  MET A 461 "
    ideal  model  delta    sigma   weight residual
    1.520  1.467  0.053 3.00e-02 1.11e+03 3.10e+00
  ... (remaining 5634 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.70: 7399
        2.70 -     5.41: 225
        5.41 -     8.11: 39
        8.11 -    10.82: 5
       10.82 -    13.52: 4
  Bond angle restraints: 7672
  Sorted by residual:
  angle pdb=" C   LEU A 422 "
        pdb=" N   SER A 423 "
        pdb=" CA  SER A 423 "
      ideal   model   delta    sigma   weight residual
     122.81  136.33  -13.52 1.57e+00 4.06e-01 7.42e+01
  angle pdb=" N   LEU A 422 "
        pdb=" CA  LEU A 422 "
        pdb=" C   LEU A 422 "
      ideal   model   delta    sigma   weight residual
     110.23  122.19  -11.96 1.45e+00 4.76e-01 6.80e+01
  angle pdb=" C   ILE A 417 "
        pdb=" N   PRO A 418 "
        pdb=" CA  PRO A 418 "
      ideal   model   delta    sigma   weight residual
     119.56  127.53   -7.97 1.01e+00 9.80e-01 6.23e+01
  angle pdb=" CA  ILE A 417 "
        pdb=" C   ILE A 417 "
        pdb=" N   PRO A 418 "
      ideal   model   delta    sigma   weight residual
     120.83  116.10    4.73 6.10e-01 2.69e+00 6.01e+01
  angle pdb=" CA  LEU A 422 "
        pdb=" C   LEU A 422 "
        pdb=" N   SER A 423 "
      ideal   model   delta    sigma   weight residual
     115.85  108.31    7.54 1.29e+00 6.01e-01 3.41e+01
  ... (remaining 7667 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 3111
       17.48 -    34.97: 188
       34.97 -    52.45: 61
       52.45 -    69.93: 4
       69.93 -    87.42: 3
  Dihedral angle restraints: 3367
    sinusoidal: 1305
      harmonic: 2062
  Sorted by residual:
  dihedral pdb=" CA  HIS A 239 "
           pdb=" C   HIS A 239 "
           pdb=" N   PHE A 240 "
           pdb=" CA  PHE A 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.63   20.37     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  SER A  33 "
           pdb=" C   SER A  33 "
           pdb=" N   LEU A  34 "
           pdb=" CA  LEU A  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.64  -19.36     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" N   TYR A 703 "
           pdb=" C   TYR A 703 "
           pdb=" CA  TYR A 703 "
           pdb=" CB  TYR A 703 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.52   -8.72     0      2.50e+00 1.60e-01 1.22e+01
  ... (remaining 3364 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 808
       0.085 -    0.171: 91
       0.171 -    0.256: 11
       0.256 -    0.341: 6
       0.341 -    0.426: 1
  Chirality restraints: 917
  Sorted by residual:
  chirality pdb=" CA  LEU A 422 "
            pdb=" N   LEU A 422 "
            pdb=" C   LEU A 422 "
            pdb=" CB  LEU A 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.54e+00
  chirality pdb=" CG  LEU A 415 "
            pdb=" CB  LEU A 415 "
            pdb=" CD1 LEU A 415 "
            pdb=" CD2 LEU A 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.25   -0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" CA  TYR A 703 "
            pdb=" N   TYR A 703 "
            pdb=" C   TYR A 703 "
            pdb=" CB  TYR A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 914 not shown)

  Planarity restraints: 969
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 703 "   -0.041 2.00e-02 2.50e+03   3.70e-02 2.73e+01
        pdb=" CG  TYR A 703 "    0.091 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 703 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 703 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 703 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 703 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 703 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 703 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 720 "   -0.024 2.00e-02 2.50e+03   4.80e-02 2.31e+01
        pdb=" C   ARG A 720 "    0.083 2.00e-02 2.50e+03
        pdb=" O   ARG A 720 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   MET A 721 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 691 "   -0.024 2.00e-02 2.50e+03   4.79e-02 2.30e+01
        pdb=" C   GLY A 691 "    0.083 2.00e-02 2.50e+03
        pdb=" O   GLY A 691 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   ALA A 692 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 966 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 699
        2.74 -     3.28: 5997
        3.28 -     3.82: 8923
        3.82 -     4.36: 10012
        4.36 -     4.90: 16562
  Nonbonded interactions: 42193
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU A 422 "
            pdb=" O   SER A 423 "
     model   vdw
     2.205 3.460
  nonbonded pdb=" O   LEU A 432 "
            pdb=" NH1 ARG A 439 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" O   PRO A 407 "
            pdb=" CG2 VAL A 411 "
     model   vdw
     2.227 3.460
  nonbonded pdb=" O   LEU A 414 "
            pdb=" CD1 ILE A 417 "
     model   vdw
     2.243 3.460
  nonbonded pdb=" NH1 ARG A  65 "
            pdb=" OD1 ASN A 504 "
     model   vdw
     2.254 3.120
  ... (remaining 42188 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.500
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4091
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      :  0.004   0.053   5639  Z= 0.251
  Angle     :  1.121  13.520   7672  Z= 0.691
  Chirality :  0.061   0.426    917
  Planarity :  0.009   0.080    969
  Dihedral  : 12.529  87.415   2041
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 23.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.15 %
    Favored  : 88.98 %
  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: -2.98 (0.27), residues: 721
  helix: -1.95 (0.19), residues: 494
  sheet: -1.26 (0.95), residues: 21
  loop : -1.56 (0.42), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 736 
 HIS   0.007   0.001   HIS A  68 
 PHE   0.042   0.003   PHE A  12 
 TYR   0.091   0.005   TYR A 703 
 ARG   0.003   0.000   ARG A 501 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 156
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A   20 MET cc_start: 0.5777 (tmm) cc_final: 0.4769 (tpp)
REVERT: A   79 LYS cc_start: 0.7398 (mmpt) cc_final: 0.7192 (mmpt)
REVERT: A  307 PHE cc_start: 0.4082 (m-10) cc_final: 0.3830 (m-80)
REVERT: A  325 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7492 (pp)
REVERT: A  414 LEU cc_start: 0.0394 (OUTLIER) cc_final: -0.1126 (mp)
REVERT: A  555 ASP cc_start: 0.7868 (m-30) cc_final: 0.7652 (m-30)
REVERT: A  559 SER cc_start: 0.8509 (m) cc_final: 0.8097 (p)
REVERT: A  580 PHE cc_start: 0.6584 (t80) cc_final: 0.6160 (t80)
REVERT: A  640 TRP cc_start: 0.6175 (t-100) cc_final: 0.5698 (t-100)
REVERT: A  668 ILE cc_start: 0.4527 (tp) cc_final: 0.4168 (mm)
  outliers start: 11
  outliers final: 4
  residues processed: 165
  average time/residue: 0.1657
  time to fit residues: 35.7587
Evaluate side-chains
  117 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0470
   chunk 18 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 29 optimal weight:   30.0000
   chunk 56 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0070
   chunk 42 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   overall best weight:    2.0102

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS
A 395 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5165 r_free = 0.5165 target = 0.315083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.286447 restraints weight = 11500.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4966 r_free = 0.4966 target = 0.291840 restraints weight = 8590.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.5001 r_free = 0.5001 target = 0.296352 restraints weight = 6570.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.5009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4367
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   5639  Z= 0.225
  Angle     :  0.751   7.455   7672  Z= 0.396
  Chirality :  0.047   0.207    917
  Planarity :  0.006   0.050    969
  Dihedral  :  4.353  24.860    770
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  2.88 %
    Favored  : 96.95 %
  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: -0.09 (0.30), residues: 721
  helix:  0.33 (0.22), residues: 490
  sheet: -0.29 (0.96), residues: 21
  loop : -0.71 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 737 
 HIS   0.007   0.001   HIS A 239 
 PHE   0.023   0.002   PHE A  12 
 TYR   0.041   0.003   TYR A 703 
 ARG   0.003   0.000   ARG A  13 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A   20 MET cc_start: 0.5897 (tmm) cc_final: 0.5465 (tmm)
REVERT: A  125 MET cc_start: 0.1231 (tpt) cc_final: 0.0978 (mtm)
REVERT: A  131 ARG cc_start: 0.4894 (ttt180) cc_final: 0.4565 (ttt180)
REVERT: A  171 LEU cc_start: 0.7777 (mp) cc_final: 0.7537 (mp)
REVERT: A  307 PHE cc_start: 0.5370 (m-10) cc_final: 0.5098 (m-80)
REVERT: A  412 MET cc_start: 0.2999 (ptt) cc_final: 0.2645 (ptt)
REVERT: A  477 MET cc_start: 0.4005 (mtp) cc_final: 0.3767 (mtp)
REVERT: A  580 PHE cc_start: 0.6811 (t80) cc_final: 0.6329 (t80)
REVERT: A  640 TRP cc_start: 0.6407 (t-100) cc_final: 0.6040 (t-100)
REVERT: A  649 PHE cc_start: 0.6558 (m-10) cc_final: 0.6192 (m-80)
REVERT: A  701 MET cc_start: 0.9120 (tpp) cc_final: 0.8620 (tpp)
REVERT: A  704 LEU cc_start: 0.8344 (mt) cc_final: 0.7979 (mt)
REVERT: A  715 ASP cc_start: 0.6729 (m-30) cc_final: 0.6479 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1542
  time to fit residues: 26.5317
Evaluate side-chains
  111 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:    0.0870
   chunk 61 optimal weight:    8.9990
   chunk 7 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 56 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   overall best weight:    3.8166

-------------------------------------------------------------------------------
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 = 0.5056 r_free = 0.5056 target = 0.305240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.268049 restraints weight = 11226.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4793 r_free = 0.4793 target = 0.273773 restraints weight = 8514.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.277932 restraints weight = 6696.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.4854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4814
moved from start:          0.3721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5639  Z= 0.222
  Angle     :  0.725   7.604   7672  Z= 0.377
  Chirality :  0.044   0.184    917
  Planarity :  0.006   0.056    969
  Dihedral  :  4.349  23.408    770
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  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:  0.81 (0.31), residues: 721
  helix:  1.19 (0.23), residues: 479
  sheet:  0.28 (0.90), residues: 21
  loop : -0.79 (0.44), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 737 
 HIS   0.003   0.001   HIS A 615 
 PHE   0.027   0.002   PHE A 311 
 TYR   0.028   0.002   TYR A 703 
 ARG   0.005   0.001   ARG A 514 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A  125 MET cc_start: 0.1880 (tpt) cc_final: 0.1679 (mtt)
REVERT: A  131 ARG cc_start: 0.5208 (ttt180) cc_final: 0.5007 (ttt180)
REVERT: A  171 LEU cc_start: 0.7883 (mp) cc_final: 0.7655 (mp)
REVERT: A  461 MET cc_start: -0.1156 (tpt) cc_final: -0.2097 (tpt)
REVERT: A  555 ASP cc_start: 0.8135 (m-30) cc_final: 0.7925 (m-30)
REVERT: A  580 PHE cc_start: 0.7242 (t80) cc_final: 0.6634 (t80)
REVERT: A  631 MET cc_start: 0.7969 (ttp) cc_final: 0.7708 (ttp)
REVERT: A  640 TRP cc_start: 0.6787 (t-100) cc_final: 0.6265 (t-100)
REVERT: A  649 PHE cc_start: 0.7058 (m-10) cc_final: 0.6702 (m-80)
REVERT: A  700 MET cc_start: 0.6950 (tmm) cc_final: 0.6717 (tmm)
REVERT: A  715 ASP cc_start: 0.7350 (m-30) cc_final: 0.7035 (m-30)
REVERT: A  751 LEU cc_start: 0.8511 (pp) cc_final: 0.7758 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1503
  time to fit residues: 25.0279
Evaluate side-chains
  105 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 34 optimal weight:    7.9990
   chunk 22 optimal weight:   30.0000
   chunk 24 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:   20.0000
   chunk 19 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    3.1186

-------------------------------------------------------------------------------
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 = 0.5113 r_free = 0.5113 target = 0.309744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.275284 restraints weight = 11050.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.281011 restraints weight = 7944.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4913 r_free = 0.4913 target = 0.285238 restraints weight = 6113.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.4915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4778
moved from start:          0.4263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5639  Z= 0.211
  Angle     :  0.687   6.791   7672  Z= 0.356
  Chirality :  0.043   0.200    917
  Planarity :  0.005   0.063    969
  Dihedral  :  4.388  27.161    770
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  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:  0.88 (0.32), residues: 721
  helix:  1.18 (0.23), residues: 488
  sheet: -0.01 (0.80), residues: 21
  loop : -0.64 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 737 
 HIS   0.007   0.001   HIS A 239 
 PHE   0.018   0.002   PHE A 311 
 TYR   0.031   0.002   TYR A 703 
 ARG   0.003   0.000   ARG A 740 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A  125 MET cc_start: 0.1695 (tpt) cc_final: 0.1437 (tmm)
REVERT: A  131 ARG cc_start: 0.5180 (ttt180) cc_final: 0.3992 (ttt90)
REVERT: A  132 HIS cc_start: 0.7963 (m90) cc_final: 0.7598 (m90)
REVERT: A  171 LEU cc_start: 0.7769 (mp) cc_final: 0.7541 (mp)
REVERT: A  477 MET cc_start: 0.3865 (mtp) cc_final: 0.3483 (mtp)
REVERT: A  563 LYS cc_start: 0.8909 (mmpt) cc_final: 0.8591 (mmmt)
REVERT: A  580 PHE cc_start: 0.7288 (t80) cc_final: 0.6796 (t80)
REVERT: A  640 TRP cc_start: 0.6606 (t-100) cc_final: 0.6103 (t-100)
REVERT: A  649 PHE cc_start: 0.7036 (m-10) cc_final: 0.6659 (m-80)
REVERT: A  715 ASP cc_start: 0.7046 (m-30) cc_final: 0.6723 (m-30)
REVERT: A  751 LEU cc_start: 0.8462 (pp) cc_final: 0.7831 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1603
  time to fit residues: 25.7988
Evaluate side-chains
  101 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 18 optimal weight:   40.0000
   chunk 49 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0070
   chunk 39 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    2.4004

-------------------------------------------------------------------------------
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 = 0.5102 r_free = 0.5102 target = 0.308674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4807 r_free = 0.4807 target = 0.273416 restraints weight = 10798.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4850 r_free = 0.4850 target = 0.279208 restraints weight = 7848.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.283426 restraints weight = 6114.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.4914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4817
moved from start:          0.4712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5639  Z= 0.180
  Angle     :  0.665   6.680   7672  Z= 0.344
  Chirality :  0.043   0.192    917
  Planarity :  0.005   0.058    969
  Dihedral  :  4.288  22.925    770
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.96 (0.32), residues: 721
  helix:  1.26 (0.24), residues: 489
  sheet: -0.17 (0.82), residues: 21
  loop : -0.64 (0.46), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 737 
 HIS   0.006   0.001   HIS A 239 
 PHE   0.025   0.002   PHE A 311 
 TYR   0.030   0.002   TYR A 703 
 ARG   0.011   0.000   ARG A 281 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A  131 ARG cc_start: 0.4844 (ttt180) cc_final: 0.3963 (ttt90)
REVERT: A  132 HIS cc_start: 0.7870 (m90) cc_final: 0.7613 (m90)
REVERT: A  477 MET cc_start: 0.3807 (mtp) cc_final: 0.3492 (mtp)
REVERT: A  563 LYS cc_start: 0.8994 (mmpt) cc_final: 0.8733 (mmmt)
REVERT: A  579 MET cc_start: 0.7941 (mmt) cc_final: 0.7686 (tpt)
REVERT: A  580 PHE cc_start: 0.7410 (t80) cc_final: 0.7070 (t80)
REVERT: A  640 TRP cc_start: 0.6720 (t-100) cc_final: 0.6180 (t-100)
REVERT: A  649 PHE cc_start: 0.7162 (m-10) cc_final: 0.6909 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1680
  time to fit residues: 26.0281
Evaluate side-chains
  98 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:   40.0000
   chunk 13 optimal weight:    0.3980
   chunk 67 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0670
   chunk 25 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0470
   chunk 52 optimal weight:   20.0000
   overall best weight:    0.9020

-------------------------------------------------------------------------------
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 = 0.5121 r_free = 0.5121 target = 0.310834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.278637 restraints weight = 11027.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4898 r_free = 0.4898 target = 0.283929 restraints weight = 8094.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.287792 restraints weight = 6220.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.4941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4736
moved from start:          0.4886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5639  Z= 0.158
  Angle     :  0.647   6.552   7672  Z= 0.333
  Chirality :  0.042   0.188    917
  Planarity :  0.005   0.057    969
  Dihedral  :  4.220  24.060    770
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.08 (0.32), residues: 721
  helix:  1.37 (0.24), residues: 487
  sheet: -0.58 (0.80), residues: 21
  loop : -0.58 (0.45), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 737 
 HIS   0.004   0.001   HIS A 239 
 PHE   0.014   0.001   PHE A 611 
 TYR   0.025   0.001   TYR A 703 
 ARG   0.007   0.000   ARG A 653 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A  563 LYS cc_start: 0.8926 (mmpt) cc_final: 0.8686 (mmmt)
REVERT: A  566 LEU cc_start: 0.8454 (mt) cc_final: 0.8131 (mp)
REVERT: A  640 TRP cc_start: 0.6713 (t-100) cc_final: 0.6173 (t-100)
REVERT: A  649 PHE cc_start: 0.7110 (m-10) cc_final: 0.6853 (m-80)
REVERT: A  700 MET cc_start: 0.6710 (tmm) cc_final: 0.6499 (tmm)
REVERT: A  715 ASP cc_start: 0.7326 (m-30) cc_final: 0.6986 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1434
  time to fit residues: 22.4768
Evaluate side-chains
  104 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 64 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 50 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 68 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 18 optimal weight:   40.0000
   chunk 66 optimal weight:   40.0000
   chunk 3 optimal weight:   20.0000
   overall best weight:    4.1986

-------------------------------------------------------------------------------
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 = 0.5090 r_free = 0.5090 target = 0.306321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4843 r_free = 0.4843 target = 0.276378 restraints weight = 11294.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4861 r_free = 0.4861 target = 0.280245 restraints weight = 8582.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.283223 restraints weight = 6762.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.4888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4970
moved from start:          0.5502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5639  Z= 0.221
  Angle     :  0.743   7.097   7672  Z= 0.386
  Chirality :  0.044   0.183    917
  Planarity :  0.005   0.056    969
  Dihedral  :  4.454  22.983    770
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  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:  0.98 (0.32), residues: 721
  helix:  1.28 (0.24), residues: 491
  sheet: -0.37 (0.94), residues: 21
  loop : -0.64 (0.47), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 111 
 HIS   0.007   0.002   HIS A 239 
 PHE   0.027   0.002   PHE A 311 
 TYR   0.026   0.002   TYR A 703 
 ARG   0.016   0.001   ARG A 281 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A  131 ARG cc_start: 0.5328 (ttt180) cc_final: 0.4555 (ttt180)
REVERT: A  398 MET cc_start: 0.3066 (tpt) cc_final: 0.2646 (tpp)
REVERT: A  463 ARG cc_start: 0.6241 (mtt90) cc_final: 0.5762 (mmt90)
REVERT: A  555 ASP cc_start: 0.8435 (m-30) cc_final: 0.8166 (m-30)
REVERT: A  563 LYS cc_start: 0.8948 (mmpt) cc_final: 0.8745 (mmmt)
REVERT: A  580 PHE cc_start: 0.7527 (t80) cc_final: 0.7327 (t80)
REVERT: A  640 TRP cc_start: 0.6774 (t-100) cc_final: 0.6109 (t-100)
REVERT: A  649 PHE cc_start: 0.7161 (m-10) cc_final: 0.6929 (m-80)
REVERT: A  700 MET cc_start: 0.6787 (tmm) cc_final: 0.6578 (tmm)
REVERT: A  751 LEU cc_start: 0.8074 (pp) cc_final: 0.7369 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1533
  time to fit residues: 24.1566
Evaluate side-chains
  107 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0970
   chunk 69 optimal weight:   20.0000
   chunk 20 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:   50.0000
   chunk 68 optimal weight:    0.4980
   overall best weight:    2.1184

-------------------------------------------------------------------------------
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 = 0.5104 r_free = 0.5104 target = 0.307792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4849 r_free = 0.4849 target = 0.277591 restraints weight = 11218.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4874 r_free = 0.4874 target = 0.281279 restraints weight = 8394.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.283423 restraints weight = 6947.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.4878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4914
moved from start:          0.5663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5639  Z= 0.167
  Angle     :  0.676   7.089   7672  Z= 0.345
  Chirality :  0.043   0.193    917
  Planarity :  0.005   0.056    969
  Dihedral  :  4.303  23.554    770
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.04 (0.32), residues: 721
  helix:  1.38 (0.24), residues: 487
  sheet: -0.63 (0.96), residues: 21
  loop : -0.68 (0.46), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 737 
 HIS   0.005   0.001   HIS A 239 
 PHE   0.019   0.001   PHE A 311 
 TYR   0.023   0.001   TYR A 703 
 ARG   0.007   0.001   ARG A 281 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A    1 MET cc_start: 0.7479 (tmm) cc_final: 0.7137 (tmm)
REVERT: A  131 ARG cc_start: 0.4930 (ttt180) cc_final: 0.4260 (ttt180)
REVERT: A  400 ARG cc_start: 0.6736 (mmm160) cc_final: 0.4077 (mmt180)
REVERT: A  555 ASP cc_start: 0.8320 (m-30) cc_final: 0.8120 (m-30)
REVERT: A  566 LEU cc_start: 0.8426 (mt) cc_final: 0.8116 (mp)
REVERT: A  640 TRP cc_start: 0.6744 (t-100) cc_final: 0.6148 (t-100)
REVERT: A  649 PHE cc_start: 0.7033 (m-10) cc_final: 0.6787 (m-80)
REVERT: A  662 MET cc_start: -0.4924 (mmt) cc_final: -0.5202 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1589
  time to fit residues: 24.8061
Evaluate side-chains
  104 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:   50.0000
   chunk 66 optimal weight:   30.0000
   chunk 64 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 68 optimal weight:   30.0000
   chunk 5 optimal weight:   20.0000
   chunk 44 optimal weight:    8.9990
   chunk 16 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 53 optimal weight:   20.0000
   overall best weight:    6.9792

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

Flipped N/Q/H residues before XYZ refinement:
** A  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 ASN
** A 554 GLN ** 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 = 0.5018 r_free = 0.5018 target = 0.297323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4829 r_free = 0.4829 target = 0.273621 restraints weight = 11347.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.276140 restraints weight = 10004.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4859 r_free = 0.4859 target = 0.278439 restraints weight = 8105.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.4859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5071
moved from start:          0.6659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   5639  Z= 0.328
  Angle     :  0.875  10.412   7672  Z= 0.454
  Chirality :  0.050   0.350    917
  Planarity :  0.006   0.057    969
  Dihedral  :  5.327  34.982    770
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.13 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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:  0.49 (0.32), residues: 721
  helix:  1.04 (0.24), residues: 483
  sheet: -1.14 (0.98), residues: 22
  loop : -1.06 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP A 111 
 HIS   0.010   0.002   HIS A 239 
 PHE   0.019   0.003   PHE A 611 
 TYR   0.030   0.003   TYR A 703 
 ARG   0.007   0.001   ARG A 463 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A    1 MET cc_start: 0.7631 (tmm) cc_final: 0.7081 (tmm)
REVERT: A  127 THR cc_start: 0.6124 (t) cc_final: 0.5771 (m)
REVERT: A  269 ILE cc_start: 0.5527 (mm) cc_final: 0.5222 (mm)
REVERT: A  398 MET cc_start: 0.3258 (tpt) cc_final: 0.2691 (tpp)
REVERT: A  461 MET cc_start: -0.0047 (tmm) cc_final: -0.0535 (tmm)
REVERT: A  463 ARG cc_start: 0.6995 (mmt90) cc_final: 0.6457 (mmt90)
REVERT: A  631 MET cc_start: 0.8206 (ttp) cc_final: 0.7903 (ttp)
REVERT: A  640 TRP cc_start: 0.6319 (t-100) cc_final: 0.5750 (t-100)
REVERT: A  737 TRP cc_start: 0.5359 (t60) cc_final: 0.4711 (t60)
REVERT: A  751 LEU cc_start: 0.7759 (pp) cc_final: 0.7075 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1509
  time to fit residues: 22.8336
Evaluate side-chains
  104 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0570
   chunk 65 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 60 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    3.1904

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

Flipped N/Q/H residues before XYZ refinement:
** A  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4993 r_free = 0.4993 target = 0.298150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4797 r_free = 0.4797 target = 0.272274 restraints weight = 11020.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4813 r_free = 0.4813 target = 0.276239 restraints weight = 10106.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4831 r_free = 0.4831 target = 0.278435 restraints weight = 7080.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.4808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4954
moved from start:          0.6714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5639  Z= 0.209
  Angle     :  0.766   8.505   7672  Z= 0.389
  Chirality :  0.046   0.262    917
  Planarity :  0.006   0.062    969
  Dihedral  :  4.931  28.480    770
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  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:  0.60 (0.32), residues: 721
  helix:  1.09 (0.23), residues: 484
  sheet: -1.06 (1.03), residues: 21
  loop : -0.92 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 111 
 HIS   0.005   0.002   HIS A 239 
 PHE   0.027   0.002   PHE A 649 
 TYR   0.024   0.002   TYR A 703 
 ARG   0.009   0.001   ARG A 281 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A  269 ILE cc_start: 0.5436 (mm) cc_final: 0.5167 (mm)
REVERT: A  398 MET cc_start: 0.2952 (tpt) cc_final: 0.2526 (tpp)
REVERT: A  412 MET cc_start: 0.4025 (ptt) cc_final: 0.3727 (ptt)
REVERT: A  463 ARG cc_start: 0.6906 (mmt90) cc_final: 0.6552 (mmt-90)
REVERT: A  555 ASP cc_start: 0.8310 (m-30) cc_final: 0.8104 (m-30)
REVERT: A  631 MET cc_start: 0.8147 (ttp) cc_final: 0.7907 (ttp)
REVERT: A  640 TRP cc_start: 0.6575 (t-100) cc_final: 0.5956 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1519
  time to fit residues: 22.4407
Evaluate side-chains
  99 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 5 optimal weight:   30.0000
   chunk 65 optimal weight:    8.9990
   chunk 60 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
** A 162 ASN ** 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 = 0.5027 r_free = 0.5027 target = 0.298151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4829 r_free = 0.4829 target = 0.272830 restraints weight = 11897.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4859 r_free = 0.4859 target = 0.279117 restraints weight = 10083.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.280739 restraints weight = 6318.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.4858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4990
moved from start:          0.7041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5639  Z= 0.223
  Angle     :  0.772   8.902   7672  Z= 0.393
  Chirality :  0.046   0.249    917
  Planarity :  0.006   0.063    969
  Dihedral  :  4.968  28.358    770
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  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:  0.57 (0.32), residues: 721
  helix:  1.11 (0.24), residues: 483
  sheet: -1.27 (1.04), residues: 21
  loop : -1.02 (0.46), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 111 
 HIS   0.006   0.002   HIS A 239 
 PHE   0.041   0.002   PHE A 649 
 TYR   0.025   0.002   TYR A 703 
 ARG   0.008   0.001   ARG A 281 

===============================================================================
Job complete
usr+sys time: 1810.73 seconds
wall clock time: 32 minutes 59.55 seconds (1979.55 seconds total)