Starting phenix.real_space_refine
on Sun May  3 02:18:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k8d_22728/05_2026/7k8d_22728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k8d_22728/05_2026/7k8d_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_22728/05_2026/7k8d_22728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k8d_22728/05_2026/7k8d_22728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k8d_22728/05_2026/7k8d_22728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k8d_22728/05_2026/7k8d_22728.cif"
  }
  resolution = 4.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/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: 1.55, per 1000 atoms: 0.28
  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: 0.38
  Conformation dependent library (CDL) restraints added in 325.1 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: 0.16
  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: 0.84

  Time building geometry restraints manager: 0.54 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:                         0.000
  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:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.080
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.570
-------------------------------------------------------------------------------
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= 0.236
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG A 501 
 TYR   0.091   0.005   TYR A 703 
 PHE   0.042   0.003   PHE A  12 
 TRP   0.036   0.002   TRP A 736 
 HIS   0.007   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 5639)
  covalent geometry    : angle       1.12074 ( 7672)
  hydrogen bonds       : bond        0.14872 (  396)
  hydrogen bonds       : angle       7.37256 ( 1149)

*********************** 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  : 0.191 
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: 0.4766 (tpp)
REVERT: A   79 LYS cc_start: 0.7398 (mmpt) cc_final: 0.7191 (mmpt)
REVERT: A  325 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7490 (pp)
REVERT: A  414 LEU cc_start: 0.0394 (OUTLIER) cc_final: -0.1125 (mp)
REVERT: A  555 ASP cc_start: 0.7868 (m-30) cc_final: 0.7654 (m-30)
REVERT: A  580 PHE cc_start: 0.6584 (t80) cc_final: 0.6157 (t80)
REVERT: A  640 TRP cc_start: 0.6175 (t-100) cc_final: 0.5694 (t-100)
REVERT: A  668 ILE cc_start: 0.4527 (tp) cc_final: 0.4152 (mm)
  outliers start: 11
  outliers final: 4
  residues processed: 165
  average time/residue: 0.0728
  time to fit residues: 15.9131
Evaluate side-chains
  115 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    4.1990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5094 r_free = 0.5094 target = 0.310782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4848 r_free = 0.4848 target = 0.279382 restraints weight = 10777.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4887 r_free = 0.4887 target = 0.284335 restraints weight = 8227.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4920 r_free = 0.4920 target = 0.288700 restraints weight = 6518.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4938 r_free = 0.4938 target = 0.291193 restraints weight = 5238.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4960 r_free = 0.4960 target = 0.293892 restraints weight = 4397.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.5068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4500
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   5639  Z= 0.201
  Angle     :  0.798   7.752   7672  Z= 0.423
  Chirality :  0.047   0.213    917
  Planarity :  0.006   0.050    969
  Dihedral  :  4.529  26.514    770
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.30), residues: 721
  helix:  0.40 (0.22), residues: 481
  sheet: -0.27 (1.00), residues: 21
  loop : -0.85 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 188 
 TYR   0.035   0.003   TYR A 703 
 PHE   0.025   0.002   PHE A  12 
 TRP   0.024   0.002   TRP A 737 
 HIS   0.007   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 5639)
  covalent geometry    : angle       0.79818 ( 7672)
  hydrogen bonds       : bond        0.04922 (  396)
  hydrogen bonds       : angle       5.29958 ( 1149)

*********************** 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
  124 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.229 
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: 0.6009 (tmm) cc_final: 0.5560 (tmm)
REVERT: A  131 ARG cc_start: 0.4959 (ttt180) cc_final: 0.4293 (ttt180)
REVERT: A  171 LEU cc_start: 0.7948 (mp) cc_final: 0.7727 (mp)
REVERT: A  284 MET cc_start: 0.3076 (ppp) cc_final: 0.2866 (ppp)
REVERT: A  412 MET cc_start: 0.3267 (ptt) cc_final: 0.2864 (ptt)
REVERT: A  477 MET cc_start: 0.3865 (mtp) cc_final: 0.3584 (mtp)
REVERT: A  563 LYS cc_start: 0.8915 (mmpt) cc_final: 0.8655 (mmmt)
REVERT: A  580 PHE cc_start: 0.6987 (t80) cc_final: 0.6420 (t80)
REVERT: A  631 MET cc_start: 0.7872 (ttp) cc_final: 0.7604 (ttp)
REVERT: A  640 TRP cc_start: 0.6591 (t-100) cc_final: 0.6157 (t-100)
REVERT: A  649 PHE cc_start: 0.6806 (m-10) cc_final: 0.6444 (m-80)
REVERT: A  701 MET cc_start: 0.9188 (tpp) cc_final: 0.8867 (tpp)
REVERT: A  704 LEU cc_start: 0.8317 (mt) cc_final: 0.8051 (mt)
REVERT: A  715 ASP cc_start: 0.7003 (m-30) cc_final: 0.6755 (m-30)
REVERT: A  751 LEU cc_start: 0.8459 (pp) cc_final: 0.7781 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0650
  time to fit residues: 11.0160
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  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:   40.0000
   chunk 11 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 28 optimal weight:   30.0000
   chunk 63 optimal weight:    8.9990
   chunk 32 optimal weight:    7.9990
   chunk 39 optimal weight:   20.0000
   chunk 68 optimal weight:    7.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.5073 r_free = 0.5073 target = 0.304054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4853 r_free = 0.4853 target = 0.276448 restraints weight = 11042.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.280096 restraints weight = 9468.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.283552 restraints weight = 6926.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4914 r_free = 0.4914 target = 0.286581 restraints weight = 5051.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.288305 restraints weight = 4055.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4791
moved from start:          0.4524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   5639  Z= 0.215
  Angle     :  0.813   7.897   7672  Z= 0.425
  Chirality :  0.047   0.184    917
  Planarity :  0.006   0.062    969
  Dihedral  :  4.772  29.513    770
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.78 %
    Favored  : 92.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.31), residues: 721
  helix:  0.83 (0.23), residues: 487
  sheet:  0.02 (0.84), residues: 21
  loop : -0.75 (0.47), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 514 
 TYR   0.033   0.003   TYR A 703 
 PHE   0.031   0.003   PHE A 311 
 TRP   0.035   0.003   TRP A 737 
 HIS   0.005   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 5639)
  covalent geometry    : angle       0.81273 ( 7672)
  hydrogen bonds       : bond        0.05059 (  396)
  hydrogen bonds       : angle       5.04514 ( 1149)

*********************** 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
  118 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.143 
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  131 ARG cc_start: 0.5659 (ttt180) cc_final: 0.4923 (ttt180)
REVERT: A  171 LEU cc_start: 0.7789 (mp) cc_final: 0.7573 (mp)
REVERT: A  461 MET cc_start: -0.0374 (tpt) cc_final: -0.1237 (tpt)
REVERT: A  555 ASP cc_start: 0.8332 (m-30) cc_final: 0.8097 (m-30)
REVERT: A  563 LYS cc_start: 0.9108 (mmpt) cc_final: 0.8646 (mmmt)
REVERT: A  580 PHE cc_start: 0.7261 (t80) cc_final: 0.6704 (t80)
REVERT: A  640 TRP cc_start: 0.6246 (t-100) cc_final: 0.5911 (t-100)
REVERT: A  649 PHE cc_start: 0.6943 (m-10) cc_final: 0.6643 (m-80)
REVERT: A  662 MET cc_start: -0.4385 (mmt) cc_final: -0.4725 (mmt)
  outliers start: 2
  outliers final: 1
  residues processed: 117
  average time/residue: 0.0657
  time to fit residues: 10.5475
Evaluate side-chains
  104 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 20 optimal weight:    0.4980
   chunk 0 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    2.8386

-------------------------------------------------------------------------------
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 = 0.5083 r_free = 0.5083 target = 0.306303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.271164 restraints weight = 10847.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4827 r_free = 0.4827 target = 0.276346 restraints weight = 7951.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4862 r_free = 0.4862 target = 0.280828 restraints weight = 6253.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4883 r_free = 0.4883 target = 0.283689 restraints weight = 5085.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4905 r_free = 0.4905 target = 0.286340 restraints weight = 4277.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.4923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4830
moved from start:          0.4866

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= 0.152
  Angle     :  0.702   6.784   7672  Z= 0.364
  Chirality :  0.044   0.207    917
  Planarity :  0.005   0.070    969
  Dihedral  :  4.579  24.639    770
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.32), residues: 721
  helix:  1.03 (0.23), residues: 487
  sheet: -0.30 (0.80), residues: 21
  loop : -0.74 (0.47), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 281 
 TYR   0.033   0.002   TYR A 703 
 PHE   0.027   0.002   PHE A 311 
 TRP   0.035   0.002   TRP A 111 
 HIS   0.007   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 5639)
  covalent geometry    : angle       0.70155 ( 7672)
  hydrogen bonds       : bond        0.04320 (  396)
  hydrogen bonds       : angle       4.76608 ( 1149)

*********************** 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
  115 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.197 
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: 0.4747 (tmm) cc_final: 0.4403 (tmm)
REVERT: A  131 ARG cc_start: 0.5027 (ttt180) cc_final: 0.4386 (ttt180)
REVERT: A  477 MET cc_start: 0.3619 (mtp) cc_final: 0.3384 (mtp)
REVERT: A  555 ASP cc_start: 0.8292 (m-30) cc_final: 0.7990 (m-30)
REVERT: A  563 LYS cc_start: 0.9014 (mmpt) cc_final: 0.8648 (mmmt)
REVERT: A  580 PHE cc_start: 0.7529 (t80) cc_final: 0.7100 (t80)
REVERT: A  640 TRP cc_start: 0.6547 (t-100) cc_final: 0.6108 (t-100)
REVERT: A  649 PHE cc_start: 0.7085 (m-10) cc_final: 0.6722 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0734
  time to fit residues: 11.2449
Evaluate side-chains
  100 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:   20.0000
   chunk 49 optimal weight:   20.0000
   chunk 41 optimal weight:    7.9990
   chunk 24 optimal weight:    0.2980
   chunk 65 optimal weight:   20.0000
   chunk 12 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   chunk 32 optimal weight:    8.9990
   chunk 69 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   overall best weight:    6.4588

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5028 r_free = 0.5028 target = 0.299019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4814 r_free = 0.4814 target = 0.271614 restraints weight = 11615.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4825 r_free = 0.4825 target = 0.275083 restraints weight = 10058.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.278055 restraints weight = 7363.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4860 r_free = 0.4860 target = 0.280049 restraints weight = 5033.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.281234 restraints weight = 4444.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.4862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5016
moved from start:          0.5939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   5639  Z= 0.222
  Angle     :  0.823   8.251   7672  Z= 0.433
  Chirality :  0.046   0.195    917
  Planarity :  0.007   0.105    969
  Dihedral  :  5.265  42.579    770
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.32), residues: 721
  helix:  0.90 (0.24), residues: 484
  sheet: -0.69 (0.95), residues: 21
  loop : -1.07 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 281 
 TYR   0.029   0.003   TYR A 703 
 PHE   0.019   0.002   PHE A 449 
 TRP   0.031   0.002   TRP A 111 
 HIS   0.014   0.003   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 5639)
  covalent geometry    : angle       0.82258 ( 7672)
  hydrogen bonds       : bond        0.05170 (  396)
  hydrogen bonds       : angle       5.07401 ( 1149)

*********************** 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
  116 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.207 
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: 0.5800 (ttt180) cc_final: 0.5473 (ttt180)
REVERT: A  398 MET cc_start: 0.3417 (tpt) cc_final: 0.2955 (tpp)
REVERT: A  400 ARG cc_start: 0.7067 (mmm160) cc_final: 0.5074 (mmt180)
REVERT: A  563 LYS cc_start: 0.9142 (mmpt) cc_final: 0.8745 (mmmt)
REVERT: A  580 PHE cc_start: 0.7145 (t80) cc_final: 0.6877 (t80)
REVERT: A  631 MET cc_start: 0.8080 (ttp) cc_final: 0.7764 (ttp)
REVERT: A  640 TRP cc_start: 0.6366 (t-100) cc_final: 0.5872 (t-100)
REVERT: A  649 PHE cc_start: 0.7057 (m-10) cc_final: 0.6857 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0724
  time to fit residues: 11.1989
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  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 25 optimal weight:   20.0000
   chunk 3 optimal weight:   30.0000
   chunk 30 optimal weight:    0.0010
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   overall best weight:    2.3992

-------------------------------------------------------------------------------
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 = 0.5066 r_free = 0.5066 target = 0.302725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4818 r_free = 0.4818 target = 0.272613 restraints weight = 11253.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4831 r_free = 0.4831 target = 0.274824 restraints weight = 8824.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.278616 restraints weight = 7125.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4875 r_free = 0.4875 target = 0.280808 restraints weight = 5440.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4897 r_free = 0.4897 target = 0.283892 restraints weight = 4546.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.4884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4955
moved from start:          0.6002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5639  Z= 0.148
  Angle     :  0.736  12.101   7672  Z= 0.374
  Chirality :  0.044   0.191    917
  Planarity :  0.005   0.070    969
  Dihedral  :  4.794  26.417    770
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.33), residues: 721
  helix:  1.11 (0.24), residues: 483
  sheet: -1.32 (0.91), residues: 21
  loop : -0.94 (0.46), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 281 
 TYR   0.027   0.002   TYR A 703 
 PHE   0.019   0.002   PHE A 311 
 TRP   0.033   0.002   TRP A 737 
 HIS   0.005   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5639)
  covalent geometry    : angle       0.73584 ( 7672)
  hydrogen bonds       : bond        0.04513 (  396)
  hydrogen bonds       : angle       4.78433 ( 1149)

*********************** 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
  120 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.193 
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  131 ARG cc_start: 0.4824 (ttt180) cc_final: 0.4133 (ttt180)
REVERT: A  265 PHE cc_start: 0.4299 (t80) cc_final: 0.3916 (t80)
REVERT: A  398 MET cc_start: 0.2621 (tpt) cc_final: 0.2396 (tpp)
REVERT: A  400 ARG cc_start: 0.6791 (mmm160) cc_final: 0.4318 (mmt180)
REVERT: A  563 LYS cc_start: 0.9050 (mmpt) cc_final: 0.8728 (mmmt)
REVERT: A  631 MET cc_start: 0.8127 (ttp) cc_final: 0.7918 (ttp)
REVERT: A  640 TRP cc_start: 0.6754 (t-100) cc_final: 0.6182 (t-100)
REVERT: A  751 LEU cc_start: 0.8134 (pp) cc_final: 0.7448 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0737
  time to fit residues: 11.8927
Evaluate side-chains
  103 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 42 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 33 optimal weight:   30.0000
   chunk 36 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 23 optimal weight:   20.0000
   chunk 66 optimal weight:   30.0000
   chunk 27 optimal weight:    6.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 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 = 0.4986 r_free = 0.4986 target = 0.293037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4782 r_free = 0.4782 target = 0.266530 restraints weight = 10704.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4789 r_free = 0.4789 target = 0.268962 restraints weight = 10263.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4819 r_free = 0.4819 target = 0.272747 restraints weight = 8053.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4821 r_free = 0.4821 target = 0.273486 restraints weight = 5148.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4829 r_free = 0.4829 target = 0.274567 restraints weight = 4194.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.4838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5119
moved from start:          0.6771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   5639  Z= 0.231
  Angle     :  0.835   9.428   7672  Z= 0.439
  Chirality :  0.047   0.204    917
  Planarity :  0.006   0.077    969
  Dihedral  :  5.377  30.937    770
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 18.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.32), residues: 721
  helix:  0.92 (0.24), residues: 480
  sheet: -1.30 (0.73), residues: 31
  loop : -1.42 (0.46), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  13 
 TYR   0.028   0.003   TYR A 703 
 PHE   0.030   0.003   PHE A 649 
 TRP   0.037   0.002   TRP A 737 
 HIS   0.011   0.003   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 5639)
  covalent geometry    : angle       0.83537 ( 7672)
  hydrogen bonds       : bond        0.05139 (  396)
  hydrogen bonds       : angle       5.07695 ( 1149)

*********************** 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
  111 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.190 
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    2 PHE cc_start: 0.5225 (m-80) cc_final: 0.4983 (m-80)
REVERT: A  130 LEU cc_start: 0.7978 (mp) cc_final: 0.7359 (tt)
REVERT: A  265 PHE cc_start: 0.4860 (t80) cc_final: 0.4324 (t80)
REVERT: A  269 ILE cc_start: 0.5680 (mm) cc_final: 0.4904 (tt)
REVERT: A  398 MET cc_start: 0.3322 (tpt) cc_final: 0.2830 (tpp)
REVERT: A  463 ARG cc_start: 0.7073 (mpt90) cc_final: 0.6341 (mpt90)
REVERT: A  566 LEU cc_start: 0.8392 (mt) cc_final: 0.8104 (mp)
REVERT: A  631 MET cc_start: 0.8235 (ttp) cc_final: 0.7890 (ttp)
REVERT: A  640 TRP cc_start: 0.6402 (t-100) cc_final: 0.5955 (t-100)
REVERT: A  737 TRP cc_start: 0.5614 (t60) cc_final: 0.5032 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0703
  time to fit residues: 10.4539
Evaluate side-chains
  102 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 61 optimal weight:    9.9990
   chunk 5 optimal weight:   30.0000
   chunk 47 optimal weight:   30.0000
   chunk 10 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 69 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 54 optimal weight:    7.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** 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 = 0.4964 r_free = 0.4964 target = 0.289454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4758 r_free = 0.4758 target = 0.263013 restraints weight = 11039.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4789 r_free = 0.4789 target = 0.268347 restraints weight = 10719.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4821 r_free = 0.4821 target = 0.272706 restraints weight = 6594.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4827 r_free = 0.4827 target = 0.273779 restraints weight = 4089.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4834 r_free = 0.4834 target = 0.274762 restraints weight = 3633.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.4841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5108
moved from start:          0.7399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5639  Z= 0.236
  Angle     :  0.872   9.579   7672  Z= 0.456
  Chirality :  0.048   0.200    917
  Planarity :  0.007   0.077    969
  Dihedral  :  5.553  33.279    770
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.32), residues: 721
  helix:  0.78 (0.24), residues: 469
  sheet: -1.95 (0.98), residues: 21
  loop : -1.64 (0.43), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 281 
 TYR   0.023   0.002   TYR A  10 
 PHE   0.050   0.003   PHE A 649 
 TRP   0.030   0.003   TRP A 737 
 HIS   0.010   0.003   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 5639)
  covalent geometry    : angle       0.87190 ( 7672)
  hydrogen bonds       : bond        0.05373 (  396)
  hydrogen bonds       : angle       5.17756 ( 1149)

*********************** 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
  112 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A  130 LEU cc_start: 0.8339 (mp) cc_final: 0.7259 (tp)
REVERT: A  265 PHE cc_start: 0.4800 (t80) cc_final: 0.4204 (t80)
REVERT: A  398 MET cc_start: 0.3633 (tpt) cc_final: 0.3139 (tpp)
REVERT: A  463 ARG cc_start: 0.7141 (mpt90) cc_final: 0.6108 (mpt90)
REVERT: A  566 LEU cc_start: 0.8340 (mt) cc_final: 0.8022 (mp)
REVERT: A  579 MET cc_start: 0.8260 (mmt) cc_final: 0.8048 (mmm)
REVERT: A  631 MET cc_start: 0.8310 (ttp) cc_final: 0.8110 (ttp)
REVERT: A  640 TRP cc_start: 0.6478 (t-100) cc_final: 0.5998 (t-100)
REVERT: A  649 PHE cc_start: 0.7334 (m-80) cc_final: 0.7006 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0722
  time to fit residues: 10.8698
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  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 47 optimal weight:   20.0000
   chunk 69 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 12 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 58 optimal weight:   30.0000
   overall best weight:    2.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5019 r_free = 0.5019 target = 0.296406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4829 r_free = 0.4829 target = 0.270751 restraints weight = 11399.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.275825 restraints weight = 10279.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.279160 restraints weight = 6363.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4886 r_free = 0.4886 target = 0.279835 restraints weight = 4377.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.280828 restraints weight = 3869.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.4884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4992
moved from start:          0.7421

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= 0.152
  Angle     :  0.771   7.798   7672  Z= 0.394
  Chirality :  0.045   0.219    917
  Planarity :  0.006   0.066    969
  Dihedral  :  5.018  24.470    770
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.32), residues: 721
  helix:  0.88 (0.24), residues: 479
  sheet: -1.97 (1.00), residues: 21
  loop : -1.33 (0.45), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 281 
 TYR   0.016   0.002   TYR A  10 
 PHE   0.042   0.002   PHE A 311 
 TRP   0.037   0.002   TRP A 737 
 HIS   0.008   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 5639)
  covalent geometry    : angle       0.77079 ( 7672)
  hydrogen bonds       : bond        0.04590 (  396)
  hydrogen bonds       : angle       4.88027 ( 1149)

*********************** 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  : 0.198 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A   20 MET cc_start: 0.6828 (tmm) cc_final: 0.6053 (tpt)
REVERT: A  130 LEU cc_start: 0.8170 (mp) cc_final: 0.7021 (tp)
REVERT: A  265 PHE cc_start: 0.4546 (t80) cc_final: 0.3880 (t80)
REVERT: A  341 LEU cc_start: 0.7057 (mt) cc_final: 0.6830 (mt)
REVERT: A  463 ARG cc_start: 0.7004 (mpt90) cc_final: 0.6190 (mpt90)
REVERT: A  480 LYS cc_start: 0.4675 (mtmm) cc_final: 0.3764 (ptmt)
REVERT: A  566 LEU cc_start: 0.8226 (mt) cc_final: 0.7943 (mp)
REVERT: A  631 MET cc_start: 0.8006 (ttp) cc_final: 0.7771 (ttp)
REVERT: A  640 TRP cc_start: 0.6471 (t-100) cc_final: 0.6043 (t-100)
REVERT: A  649 PHE cc_start: 0.7266 (m-80) cc_final: 0.6914 (m-80)
REVERT: A  654 MET cc_start: 0.2152 (mmp) cc_final: 0.1757 (mmm)
REVERT: A  704 LEU cc_start: 0.7666 (mm) cc_final: 0.7295 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0661
  time to fit residues: 10.1352
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  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 22 optimal weight:   40.0000
   chunk 32 optimal weight:   40.0000
   chunk 43 optimal weight:    8.9990
   chunk 46 optimal weight:    0.8980
   chunk 17 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 39 optimal weight:   40.0000
   chunk 29 optimal weight:   10.0000
   chunk 40 optimal weight:   40.0000
   overall best weight:    5.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** 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 = 0.4983 r_free = 0.4983 target = 0.292386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.269641 restraints weight = 9714.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.274035 restraints weight = 10423.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.275637 restraints weight = 6140.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.276317 restraints weight = 4737.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4855 r_free = 0.4855 target = 0.277380 restraints weight = 3832.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.4857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5057
moved from start:          0.7778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5639  Z= 0.200
  Angle     :  0.817   8.540   7672  Z= 0.424
  Chirality :  0.047   0.211    917
  Planarity :  0.007   0.074    969
  Dihedral  :  5.296  27.304    770
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 16.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.32), residues: 721
  helix:  0.86 (0.24), residues: 475
  sheet: -2.01 (1.02), residues: 21
  loop : -1.42 (0.44), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 281 
 TYR   0.019   0.002   TYR A  10 
 PHE   0.032   0.002   PHE A 649 
 TRP   0.033   0.002   TRP A 737 
 HIS   0.010   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 5639)
  covalent geometry    : angle       0.81698 ( 7672)
  hydrogen bonds       : bond        0.04936 (  396)
  hydrogen bonds       : angle       4.98802 ( 1149)

********************** 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
  114 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it.
REVERT: A   20 MET cc_start: 0.6615 (tmm) cc_final: 0.5775 (tpt)
REVERT: A  130 LEU cc_start: 0.8176 (mp) cc_final: 0.7157 (tp)
REVERT: A  463 ARG cc_start: 0.7304 (mpt90) cc_final: 0.6437 (mpt90)
REVERT: A  480 LYS cc_start: 0.4562 (mtmm) cc_final: 0.3565 (ptmt)
REVERT: A  488 THR cc_start: 0.8089 (p) cc_final: 0.7881 (p)
REVERT: A  566 LEU cc_start: 0.7942 (mt) cc_final: 0.7674 (mp)
REVERT: A  579 MET cc_start: 0.8111 (mmt) cc_final: 0.7907 (mmm)
REVERT: A  640 TRP cc_start: 0.6228 (t-100) cc_final: 0.5879 (t-100)
REVERT: A  649 PHE cc_start: 0.7061 (m-80) cc_final: 0.6785 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0623
  time to fit residues: 9.8455
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  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 4 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 57 optimal weight:   30.0000
   chunk 42 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
A 625 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4975 r_free = 0.4975 target = 0.292244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4767 r_free = 0.4767 target = 0.266878 restraints weight = 10320.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4803 r_free = 0.4803 target = 0.272079 restraints weight = 9990.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4823 r_free = 0.4823 target = 0.274408 restraints weight = 6184.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.275731 restraints weight = 4520.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4842 r_free = 0.4842 target = 0.276785 restraints weight = 3811.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.4873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5071
moved from start:          0.8052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5639  Z= 0.172
  Angle     :  0.780   7.176   7672  Z= 0.402
  Chirality :  0.046   0.212    917
  Planarity :  0.006   0.070    969
  Dihedral  :  5.220  25.053    770
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.32), residues: 721
  helix:  0.90 (0.24), residues: 477
  sheet: -2.29 (0.92), residues: 21
  loop : -1.42 (0.44), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 281 
 TYR   0.022   0.002   TYR A 703 
 PHE   0.029   0.002   PHE A 649 
 TRP   0.034   0.002   TRP A 737 
 HIS   0.009   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5639)
  covalent geometry    : angle       0.77957 ( 7672)
  hydrogen bonds       : bond        0.04747 (  396)
  hydrogen bonds       : angle       4.93010 ( 1149)

===============================================================================
Job complete
usr+sys time: 974.66 seconds
wall clock time: 17 minutes 32.86 seconds (1052.86 seconds total)