Starting phenix.real_space_refine
on Thu Mar  6 09:34:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dmf_27535/03_2025/8dmf_27535.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dmf_27535/03_2025/8dmf_27535.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dmf_27535/03_2025/8dmf_27535.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dmf_27535/03_2025/8dmf_27535.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dmf_27535/03_2025/8dmf_27535.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dmf_27535/03_2025/8dmf_27535.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      33      5.16       5
     C    3589      2.51       5
     N     951      2.21       5
     O    1093      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5670
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 718, 5637
          Classifications: {'peptide': 718}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 685}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.03, per 1000 atoms: 0.71
  Number of scatterers: 5670
  At special positions: 0
  Unit cell: (75.828, 72.624, 127.092, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      33     16.00
     P       3     15.00
     Mg      1     11.99
     O    1093      8.00
     N     951      7.00
     C    3589      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: 1.50
  Conformation dependent library (CDL) restraints added in 901.7 milliseconds
  

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1312

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 9 sheets defined
      31.5% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 7
      No H-bonds generated for 'chain 'A' and resid 5 through 7'
    Processing helix  chain 'A' and resid 21 through 33
      removed outlier: 3.531A  pdb=" N   LEU A  25 " --> pdb=" O   GLY A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 58
    Processing helix  chain 'A' and resid 87 through 98
      removed outlier: 3.626A  pdb=" N   THR A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 126
    Processing helix  chain 'A' and resid 142 through 154
    Processing helix  chain 'A' and resid 167 through 171
      removed outlier: 3.627A  pdb=" N   GLY A 170 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 200
      No H-bonds generated for 'chain 'A' and resid 198 through 200'
    Processing helix  chain 'A' and resid 201 through 220
    Processing helix  chain 'A' and resid 235 through 248
      removed outlier: 4.231A  pdb=" N   GLU A 240 " --> pdb=" O   ASP A 236 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA A 248 " --> pdb=" O   LYS A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 275
    Processing helix  chain 'A' and resid 411 through 426
    Processing helix  chain 'A' and resid 446 through 459
    Processing helix  chain 'A' and resid 555 through 557
      No H-bonds generated for 'chain 'A' and resid 555 through 557'
    Processing helix  chain 'A' and resid 558 through 571
    Processing helix  chain 'A' and resid 598 through 617
      removed outlier: 3.534A  pdb=" N   PHE A 602 " --> pdb=" O   ASN A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 646
    Processing helix  chain 'A' and resid 670 through 672
      No H-bonds generated for 'chain 'A' and resid 670 through 672'
    Processing helix  chain 'A' and resid 674 through 684
      removed outlier: 3.512A  pdb=" N   ALA A 678 " --> pdb=" O   SER A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 716
      removed outlier: 3.553A  pdb=" N   GLN A 704 " --> pdb=" O   PRO A 700 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70
      removed outlier: 6.834A  pdb=" N   LYS A  10 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   ILE A  79 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ILE A  12 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ALA A 101 " --> pdb=" O   ILE A 130 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   LEU A 132 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   ASN A 134 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   LEU A 105 " --> pdb=" O   ASN A 134 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   VAL A 159 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 9.626A  pdb=" N   CYS A 256 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 164
    Processing sheet with id=AA3, first strand: chain 'A' and resid 342 through 343
      removed outlier: 6.964A  pdb=" N   SER A 302 " --> pdb=" O   MET A 323 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 328
      removed outlier: 3.510A  pdb=" N   LEU A 361 " --> pdb=" O   VAL A 327 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 350
      removed outlier: 4.477A  pdb=" N   ILE A 347 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434
      removed outlier: 3.585A  pdb=" N   GLN A 439 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   THR A 440 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   TYR A 400 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 579 through 580
    Processing sheet with id=AA8, first strand: chain 'A' and resid 482 through 488
      removed outlier: 3.539A  pdb=" N   ALA A 482 " --> pdb=" O   VAL A 505 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   GLU A 500 " --> pdb=" O   GLY A 590 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   GLY A 590 " --> pdb=" O   GLU A 500 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   HIS A 502 " --> pdb=" O   TYR A 588 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   LYS A 542 " --> pdb=" O   VAL A 583 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   VAL A 585 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   VAL A 587 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 650 through 654
      removed outlier: 6.706A  pdb=" N   VAL A 664 " --> pdb=" O   MET A 652 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   MET A 654 " --> pdb=" O   LYS A 662 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LYS A 662 " --> pdb=" O   MET A 654 " (cutoff:3.500A)

    225 hydrogen bonds defined for protein.
    645 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: 2.05

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1743
        1.33 -     1.45: 846
        1.45 -     1.57: 3124
        1.57 -     1.69: 5
        1.69 -     1.81: 61
  Bond restraints: 5779
  Sorted by residual:
  bond pdb=" N   GLU A 476 "
       pdb=" CA  GLU A 476 "
    ideal  model  delta    sigma   weight residual
    1.452  1.488 -0.035 1.25e-02 6.40e+03 7.96e+00
  bond pdb=" N   GLU A 697 "
       pdb=" CA  GLU A 697 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.033 1.32e-02 5.74e+03 6.38e+00
  bond pdb=" N   TYR A 474 "
       pdb=" CA  TYR A 474 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.030 1.22e-02 6.72e+03 6.21e+00
  bond pdb=" N   LYS A  22 "
       pdb=" CA  LYS A  22 "
    ideal  model  delta    sigma   weight residual
    1.460  1.490 -0.030 1.22e-02 6.72e+03 6.10e+00
  bond pdb=" N   SER A 695 "
       pdb=" CA  SER A 695 "
    ideal  model  delta    sigma   weight residual
    1.455  1.484 -0.029 1.21e-02 6.83e+03 5.63e+00
  ... (remaining 5774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 7554
        1.63 -     3.26: 201
        3.26 -     4.89: 30
        4.89 -     6.52: 5
        6.52 -     8.15: 5
  Bond angle restraints: 7795
  Sorted by residual:
  angle pdb=" N   GLU A 425 "
        pdb=" CA  GLU A 425 "
        pdb=" C   GLU A 425 "
      ideal   model   delta    sigma   weight residual
     111.28  107.47    3.81 1.09e+00 8.42e-01 1.22e+01
  angle pdb=" CA  GLU A 697 "
        pdb=" C   GLU A 697 "
        pdb=" O   GLU A 697 "
      ideal   model   delta    sigma   weight residual
     121.36  118.00    3.36 1.06e+00 8.90e-01 1.00e+01
  angle pdb=" N   GLU A 424 "
        pdb=" CA  GLU A 424 "
        pdb=" C   GLU A 424 "
      ideal   model   delta    sigma   weight residual
     111.71  108.17    3.54 1.15e+00 7.56e-01 9.47e+00
  angle pdb=" CA  GLU A 476 "
        pdb=" C   GLU A 476 "
        pdb=" O   GLU A 476 "
      ideal   model   delta    sigma   weight residual
     121.82  118.12    3.70 1.21e+00 6.83e-01 9.36e+00
  angle pdb=" CA  TYR A 696 "
        pdb=" C   TYR A 696 "
        pdb=" O   TYR A 696 "
      ideal   model   delta    sigma   weight residual
     121.55  118.32    3.23 1.06e+00 8.90e-01 9.28e+00
  ... (remaining 7790 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.34: 3265
       22.34 -    44.68: 233
       44.68 -    67.02: 10
       67.02 -    89.36: 3
       89.36 -   111.70: 4
  Dihedral angle restraints: 3515
    sinusoidal: 1461
      harmonic: 2054
  Sorted by residual:
  dihedral pdb=" C8  GTP A 802 "
           pdb=" C1' GTP A 802 "
           pdb=" N9  GTP A 802 "
           pdb=" O4' GTP A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59   -7.11  111.70     1      2.00e+01 2.50e-03 3.29e+01
  dihedral pdb=" C5' GTP A 802 "
           pdb=" O5' GTP A 802 "
           pdb=" PA  GTP A 802 "
           pdb=" O3A GTP A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  178.40 -109.13     1      2.00e+01 2.50e-03 3.19e+01
  dihedral pdb=" CA  MET A 224 "
           pdb=" C   MET A 224 "
           pdb=" N   GLU A 225 "
           pdb=" CA  GLU A 225 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.71  -20.29     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 3512 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 573
       0.037 -    0.073: 172
       0.073 -    0.110: 76
       0.110 -    0.146: 22
       0.146 -    0.183: 3
  Chirality restraints: 846
  Sorted by residual:
  chirality pdb=" CB  ILE A 535 "
            pdb=" CA  ILE A 535 "
            pdb=" CG1 ILE A 535 "
            pdb=" CG2 ILE A 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.37e-01
  chirality pdb=" CA  GLU A 424 "
            pdb=" N   GLU A 424 "
            pdb=" C   GLU A 424 "
            pdb=" CB  GLU A 424 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.37e-01
  chirality pdb=" CA  ARG A 423 "
            pdb=" N   ARG A 423 "
            pdb=" C   ARG A 423 "
            pdb=" CB  ARG A 423 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.15 2.00e-01 2.50e+01 5.98e-01
  ... (remaining 843 not shown)

  Planarity restraints: 1012
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 632 "   -0.028 5.00e-02 4.00e+02   4.21e-02 2.83e+00
        pdb=" N   PRO A 633 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 633 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 633 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 276 "    0.022 5.00e-02 4.00e+02   3.37e-02 1.82e+00
        pdb=" N   PRO A 277 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 277 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 277 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  21 "   -0.005 2.00e-02 2.50e+03   1.05e-02 1.10e+00
        pdb=" C   GLY A  21 "    0.018 2.00e-02 2.50e+03
        pdb=" O   GLY A  21 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   LYS A  22 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1009 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 65
        2.56 -     3.15: 4775
        3.15 -     3.73: 9308
        3.73 -     4.32: 11920
        4.32 -     4.90: 19654
  Nonbonded interactions: 45722
  Sorted by model distance:
  nonbonded pdb="MG    MG A 801 "
            pdb=" O3A GTP A 802 "
     model   vdw
     1.977 2.170
  nonbonded pdb="MG    MG A 801 "
            pdb=" O3G GTP A 802 "
     model   vdw
     2.168 2.170
  nonbonded pdb=" N   THR A  23 "
            pdb="MG    MG A 801 "
     model   vdw
     2.183 2.250
  nonbonded pdb=" OH  TYR A 400 "
            pdb=" NH2 ARG A 402 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" NZ  LYS A 291 "
            pdb=" OH  TYR A 388 "
     model   vdw
     2.267 3.120
  ... (remaining 45717 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:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.760
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5779  Z= 0.195
  Angle     :  0.636   8.154   7795  Z= 0.347
  Chirality :  0.046   0.183    846
  Planarity :  0.004   0.042   1012
  Dihedral  : 14.277 111.705   2203
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  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: -0.20 (0.33), residues: 716
  helix:  1.11 (0.39), residues: 202
  sheet: -0.03 (0.41), residues: 195
  loop : -0.97 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 455 
 HIS   0.009   0.001   HIS A 449 
 PHE   0.011   0.001   PHE A 610 
 TYR   0.008   0.001   TYR A 696 
 ARG   0.002   0.000   ARG A 343 

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 MET cc_start: 0.8795 (ptm) cc_final: 0.8594 (ttt)
REVERT: A  251 MET cc_start: 0.8929 (tmm) cc_final: 0.8647 (tmm)
REVERT: A  263 MET cc_start: 0.8783 (mmp) cc_final: 0.8097 (mmp)
REVERT: A  323 MET cc_start: 0.8461 (mmp) cc_final: 0.8205 (mmm)
REVERT: A  563 MET cc_start: 0.9575 (mmp) cc_final: 0.9122 (mmm)
REVERT: A  650 MET cc_start: 0.9167 (mpp) cc_final: 0.8874 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.1485
  time to fit residues: 9.9784
Evaluate side-chains
  36 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0870
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0270
   chunk 36 optimal weight:   30.0000
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:   30.0000
   chunk 21 optimal weight:   20.0000
   chunk 33 optimal weight:   30.0000
   chunk 41 optimal weight:   20.0000
   chunk 64 optimal weight:    5.9990
   overall best weight:    2.2222

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 443 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.040951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.032702 restraints weight = 45742.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.033836 restraints weight = 27339.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.034650 restraints weight = 18819.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5779  Z= 0.161
  Angle     :  0.605  10.196   7795  Z= 0.301
  Chirality :  0.045   0.139    846
  Planarity :  0.004   0.038   1012
  Dihedral  :  7.572 111.381    787
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  8.32 %
    Favored  : 91.35 %
  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: -0.16 (0.32), residues: 716
  helix:  1.29 (0.37), residues: 206
  sheet: -0.11 (0.40), residues: 199
  loop : -1.00 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 429 
 HIS   0.008   0.001   HIS A 449 
 PHE   0.011   0.001   PHE A 255 
 TYR   0.012   0.001   TYR A 121 
 ARG   0.003   0.000   ARG A 402 

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.667 
Fit side-chains
REVERT: A  206 MET cc_start: 0.9251 (mmp) cc_final: 0.8970 (mmt)
REVERT: A  251 MET cc_start: 0.8837 (tmm) cc_final: 0.8611 (tmm)
REVERT: A  263 MET cc_start: 0.8539 (mmp) cc_final: 0.7882 (mmp)
REVERT: A  303 LEU cc_start: 0.9320 (mt) cc_final: 0.9054 (mt)
REVERT: A  323 MET cc_start: 0.8399 (mmp) cc_final: 0.8144 (mmm)
REVERT: A  389 LYS cc_start: 0.8643 (pttm) cc_final: 0.8085 (tppt)
REVERT: A  394 LYS cc_start: 0.9306 (tppt) cc_final: 0.9048 (tptp)
REVERT: A  563 MET cc_start: 0.9408 (mmp) cc_final: 0.9115 (mmm)
REVERT: A  650 MET cc_start: 0.9125 (mpp) cc_final: 0.8713 (mpp)
  outliers start: 2
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1883
  time to fit residues: 11.6127
Evaluate side-chains
  39 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 37 optimal weight:    0.3980
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:   20.0000
   chunk 31 optimal weight:   20.0000
   chunk 50 optimal weight:   30.0000
   chunk 38 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    6.0790

-------------------------------------------------------------------------------
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 = 0.3063 r_free = 0.3063 target = 0.039351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.031229 restraints weight = 48064.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.032303 restraints weight = 28730.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.033078 restraints weight = 19900.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5779  Z= 0.253
  Angle     :  0.607   9.240   7795  Z= 0.305
  Chirality :  0.044   0.158    846
  Planarity :  0.004   0.033   1012
  Dihedral  :  7.679 111.437    787
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 11.26 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.07 (0.32), residues: 716
  helix:  1.32 (0.36), residues: 207
  sheet:  0.02 (0.40), residues: 200
  loop : -0.99 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A 449 
 PHE   0.011   0.001   PHE A 255 
 TYR   0.014   0.001   TYR A 121 
 ARG   0.004   0.000   ARG A 239 

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 MET cc_start: 0.9317 (mmp) cc_final: 0.9041 (mmt)
REVERT: A  251 MET cc_start: 0.8897 (tmm) cc_final: 0.8654 (tmm)
REVERT: A  263 MET cc_start: 0.8732 (mmp) cc_final: 0.7986 (mmp)
REVERT: A  394 LYS cc_start: 0.9342 (tppt) cc_final: 0.9108 (tptp)
REVERT: A  422 MET cc_start: 0.9535 (mmm) cc_final: 0.9266 (mmm)
REVERT: A  563 MET cc_start: 0.9362 (mmp) cc_final: 0.9135 (mmm)
REVERT: A  567 MET cc_start: 0.9363 (mpp) cc_final: 0.9145 (mpp)
  outliers start: 8
  outliers final: 4
  residues processed: 45
  average time/residue: 0.1672
  time to fit residues: 10.6788
Evaluate side-chains
  40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  712 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 45 optimal weight:   20.0000
   chunk 33 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    4.1388

-------------------------------------------------------------------------------
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 = 0.3075 r_free = 0.3075 target = 0.039489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.031333 restraints weight = 48932.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.032431 restraints weight = 28959.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.033220 restraints weight = 19946.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5779  Z= 0.191
  Angle     :  0.586   8.927   7795  Z= 0.288
  Chirality :  0.043   0.199    846
  Planarity :  0.004   0.033   1012
  Dihedral  :  7.407 107.535    787
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 14.03 %
    Favored  : 85.48 %
  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:  0.05 (0.32), residues: 716
  helix:  1.57 (0.37), residues: 207
  sheet:  0.13 (0.43), residues: 179
  loop : -1.02 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 429 
 HIS   0.006   0.001   HIS A 449 
 PHE   0.016   0.001   PHE A 255 
 TYR   0.011   0.001   TYR A 121 
 ARG   0.004   0.000   ARG A 239 

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 MET cc_start: 0.9232 (mmp) cc_final: 0.8939 (mmt)
REVERT: A  251 MET cc_start: 0.8819 (tmm) cc_final: 0.8571 (tmm)
REVERT: A  323 MET cc_start: 0.8710 (mmm) cc_final: 0.8266 (mmm)
REVERT: A  422 MET cc_start: 0.9523 (mmm) cc_final: 0.9176 (mmm)
REVERT: A  563 MET cc_start: 0.9370 (mmp) cc_final: 0.9087 (mmm)
REVERT: A  567 MET cc_start: 0.9303 (mpp) cc_final: 0.9075 (mpp)
REVERT: A  650 MET cc_start: 0.9194 (mpp) cc_final: 0.8956 (mpp)
  outliers start: 3
  outliers final: 3
  residues processed: 38
  average time/residue: 0.1610
  time to fit residues: 8.9046
Evaluate side-chains
  38 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  712 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 715 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.039328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.031220 restraints weight = 48016.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.032297 restraints weight = 28738.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.033072 restraints weight = 19912.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   5779  Z= 0.194
  Angle     :  0.567   8.269   7795  Z= 0.281
  Chirality :  0.043   0.155    846
  Planarity :  0.003   0.032   1012
  Dihedral  :  7.335 106.558    787
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.87 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.06 (0.32), residues: 716
  helix:  1.68 (0.37), residues: 207
  sheet:  0.07 (0.43), residues: 179
  loop : -1.05 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A 449 
 PHE   0.011   0.001   PHE A 255 
 TYR   0.011   0.001   TYR A 121 
 ARG   0.003   0.000   ARG A 239 

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 MET cc_start: 0.9153 (mmp) cc_final: 0.8940 (mmp)
REVERT: A  251 MET cc_start: 0.8816 (tmm) cc_final: 0.8578 (tmm)
REVERT: A  323 MET cc_start: 0.8731 (mmm) cc_final: 0.8279 (mmm)
REVERT: A  422 MET cc_start: 0.9545 (mmm) cc_final: 0.9321 (mmm)
REVERT: A  650 MET cc_start: 0.9188 (mpp) cc_final: 0.8770 (mpp)
  outliers start: 8
  outliers final: 6
  residues processed: 40
  average time/residue: 0.1476
  time to fit residues: 8.8713
Evaluate side-chains
  40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  712 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0010
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 24 optimal weight:   20.0000
   chunk 47 optimal weight:    6.9990
   chunk 45 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    3.1792

-------------------------------------------------------------------------------
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 = 0.3088 r_free = 0.3088 target = 0.039980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.031887 restraints weight = 46505.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.032977 restraints weight = 28014.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.033737 restraints weight = 19460.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5779  Z= 0.163
  Angle     :  0.567   8.460   7795  Z= 0.278
  Chirality :  0.043   0.152    846
  Planarity :  0.003   0.033   1012
  Dihedral  :  7.160 104.689    787
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 15.17 %
    Favored  : 83.69 %
  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:  0.14 (0.33), residues: 716
  helix:  1.81 (0.38), residues: 207
  sheet:  0.13 (0.44), residues: 178
  loop : -1.05 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A 449 
 PHE   0.008   0.001   PHE A 255 
 TYR   0.009   0.001   TYR A 626 
 ARG   0.003   0.000   ARG A 239 

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.8815 (tmm) cc_final: 0.8576 (tmm)
REVERT: A  303 LEU cc_start: 0.9368 (mt) cc_final: 0.9096 (mt)
REVERT: A  323 MET cc_start: 0.8754 (mmm) cc_final: 0.8264 (mmm)
REVERT: A  422 MET cc_start: 0.9524 (mmm) cc_final: 0.9291 (mmm)
  outliers start: 7
  outliers final: 6
  residues processed: 44
  average time/residue: 0.1520
  time to fit residues: 9.6816
Evaluate side-chains
  41 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  712 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 69 optimal weight:   20.0000
   chunk 37 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   chunk 47 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 HIS ** 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 = 0.3066 r_free = 0.3066 target = 0.039390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.031307 restraints weight = 48087.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.032366 restraints weight = 28917.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.033154 restraints weight = 20147.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   5779  Z= 0.235
  Angle     :  0.616   8.710   7795  Z= 0.303
  Chirality :  0.043   0.166    846
  Planarity :  0.003   0.032   1012
  Dihedral  :  7.355 106.771    787
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 15.33 %
    Favored  : 83.20 %
  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:  0.04 (0.33), residues: 716
  helix:  1.67 (0.37), residues: 206
  sheet:  0.15 (0.43), residues: 184
  loop : -1.13 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 429 
 HIS   0.004   0.001   HIS A 449 
 PHE   0.010   0.001   PHE A 525 
 TYR   0.012   0.001   TYR A 121 
 ARG   0.003   0.000   ARG A 239 

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.8812 (tmm) cc_final: 0.8547 (tmm)
REVERT: A  323 MET cc_start: 0.8758 (mmm) cc_final: 0.8485 (mmm)
REVERT: A  422 MET cc_start: 0.9580 (mmm) cc_final: 0.9338 (mmm)
  outliers start: 9
  outliers final: 5
  residues processed: 42
  average time/residue: 0.1477
  time to fit residues: 9.2083
Evaluate side-chains
  40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  712 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 19 optimal weight:   30.0000
   chunk 34 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.038636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.030471 restraints weight = 48015.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.031528 restraints weight = 29042.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.032295 restraints weight = 20220.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5779  Z= 0.268
  Angle     :  0.668  10.187   7795  Z= 0.326
  Chirality :  0.044   0.149    846
  Planarity :  0.004   0.032   1012
  Dihedral  :  7.495 107.870    787
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 17.62 %
    Favored  : 81.08 %
  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: -0.27 (0.32), residues: 716
  helix:  1.33 (0.37), residues: 208
  sheet:  0.04 (0.43), residues: 176
  loop : -1.29 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 429 
 HIS   0.004   0.001   HIS A 449 
 PHE   0.015   0.002   PHE A 610 
 TYR   0.013   0.001   TYR A 626 
 ARG   0.003   0.000   ARG A 239 

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9395 (mm)
REVERT: A  251 MET cc_start: 0.8863 (tmm) cc_final: 0.8586 (tmm)
REVERT: A  323 MET cc_start: 0.8722 (mmm) cc_final: 0.8440 (mmm)
REVERT: A  422 MET cc_start: 0.9605 (mmm) cc_final: 0.9369 (mmm)
REVERT: A  691 MET cc_start: 0.8720 (tmm) cc_final: 0.8427 (tmm)
  outliers start: 8
  outliers final: 4
  residues processed: 42
  average time/residue: 0.1796
  time to fit residues: 10.7473
Evaluate side-chains
  40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  712 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 24 optimal weight:   30.0000
   chunk 11 optimal weight:    5.9990
   chunk 43 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 48 optimal weight:   20.0000
   chunk 29 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 488 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.039196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.030965 restraints weight = 48570.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.032045 restraints weight = 29243.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.032830 restraints weight = 20272.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5779  Z= 0.240
  Angle     :  0.663  13.500   7795  Z= 0.318
  Chirality :  0.044   0.140    846
  Planarity :  0.003   0.032   1012
  Dihedral  :  7.438 107.193    787
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 18.27 %
    Favored  : 80.91 %
  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: -0.25 (0.32), residues: 716
  helix:  1.27 (0.37), residues: 208
  sheet: -0.03 (0.43), residues: 178
  loop : -1.17 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 429 
 HIS   0.004   0.001   HIS A 449 
 PHE   0.011   0.001   PHE A 610 
 TYR   0.013   0.001   TYR A 626 
 ARG   0.002   0.000   ARG A 239 

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.9210 (mtm) cc_final: 0.8747 (mpp)
REVERT: A   95 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9399 (mm)
REVERT: A  251 MET cc_start: 0.8854 (tmm) cc_final: 0.8571 (tmm)
REVERT: A  323 MET cc_start: 0.8724 (mmm) cc_final: 0.8440 (mmm)
REVERT: A  422 MET cc_start: 0.9571 (mmm) cc_final: 0.9318 (mmm)
REVERT: A  691 MET cc_start: 0.8734 (tmm) cc_final: 0.8457 (tmm)
  outliers start: 5
  outliers final: 4
  residues processed: 39
  average time/residue: 0.1475
  time to fit residues: 8.6320
Evaluate side-chains
  40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  712 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 58 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0170
   chunk 33 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   overall best weight:    4.5424

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 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 = 0.3069 r_free = 0.3069 target = 0.039353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.031357 restraints weight = 48926.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.032414 restraints weight = 29276.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.033192 restraints weight = 20494.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5779  Z= 0.214
  Angle     :  0.672  13.188   7795  Z= 0.320
  Chirality :  0.044   0.152    846
  Planarity :  0.003   0.032   1012
  Dihedral  :  7.331 106.076    787
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 18.76 %
    Favored  : 80.59 %
  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: -0.21 (0.32), residues: 716
  helix:  1.32 (0.37), residues: 208
  sheet:  0.01 (0.43), residues: 178
  loop : -1.17 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A 449 
 PHE   0.009   0.001   PHE A 255 
 TYR   0.013   0.001   TYR A 626 
 ARG   0.002   0.000   ARG A 239 

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.8836 (tmm) cc_final: 0.8553 (tmm)
REVERT: A  303 LEU cc_start: 0.9375 (mt) cc_final: 0.9061 (mt)
REVERT: A  323 MET cc_start: 0.8724 (mmm) cc_final: 0.8423 (mmm)
REVERT: A  422 MET cc_start: 0.9559 (mmm) cc_final: 0.9303 (mmm)
REVERT: A  691 MET cc_start: 0.8753 (tmm) cc_final: 0.8473 (tmm)
  outliers start: 4
  outliers final: 4
  residues processed: 41
  average time/residue: 0.1498
  time to fit residues: 9.1766
Evaluate side-chains
  39 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  712 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 24 optimal weight:   30.0000
   chunk 19 optimal weight:    9.9990
   chunk 2 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 63 optimal weight:   20.0000
   chunk 52 optimal weight:   20.0000
   chunk 17 optimal weight:    5.9990
   chunk 55 optimal weight:   20.0000
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    6.9990

-------------------------------------------------------------------------------
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 = 0.3051 r_free = 0.3051 target = 0.038905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.030966 restraints weight = 49127.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.032021 restraints weight = 29399.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.032806 restraints weight = 20293.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5779  Z= 0.291
  Angle     :  0.710  12.907   7795  Z= 0.346
  Chirality :  0.044   0.145    846
  Planarity :  0.004   0.032   1012
  Dihedral  :  7.540 107.999    787
  Min Nonbonded Distance : 1.820

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 19.41 %
    Favored  : 79.93 %
  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: -0.35 (0.32), residues: 716
  helix:  1.16 (0.37), residues: 209
  sheet: -0.18 (0.42), residues: 189
  loop : -1.18 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 429 
 HIS   0.004   0.001   HIS A 449 
 PHE   0.015   0.002   PHE A 525 
 TYR   0.016   0.001   TYR A 626 
 ARG   0.002   0.000   ARG A 239 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1561.74 seconds
wall clock time: 28 minutes 7.83 seconds (1687.83 seconds total)