Starting phenix.real_space_refine
on Tue Mar  3 22:53:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n3p_24143/03_2026/7n3p_24143.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n3p_24143/03_2026/7n3p_24143.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n3p_24143/03_2026/7n3p_24143.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n3p_24143/03_2026/7n3p_24143.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n3p_24143/03_2026/7n3p_24143.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n3p_24143/03_2026/7n3p_24143.map"
  }
  resolution = 3.65
  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
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=   0.004 sd=   0.108
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: 5
    Type Number    sf(0)   Gaussians
     P     259      5.49       5
     S      12      5.16       5
     C    4737      2.51       5
     N    1634      2.21       5
     O    2413      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9055
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3561
          Classifications: {'peptide': 454}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 16, 'TRANS': 437}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 151
          Unresolved non-hydrogen dihedrals: 103
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 90
    Chain: "B"
      Number of atoms: 4883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 4883
          Classifications: {'RNA': 229}
          Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 14, 'rna3p_pur': 103, 'rna3p_pyr': 95}
          Link IDs: {'rna2p': 31, 'rna3p': 197}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 399
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "D"
      Number of atoms: 212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 212
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
  Time building chain proxies: 2.16, per 1000 atoms: 0.24
  Number of scatterers: 9055
  At special positions: 0
  Unit cell: (100.8, 105, 124.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P     259     15.00
     O    2413      8.00
     N    1634      7.00
     C    4737      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: 0.86
  Conformation dependent library (CDL) restraints added in 134.1 milliseconds
  

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  858

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 3 sheets defined
      58.6% alpha, 11.9% beta
      80 base pairs and 151 stacking pairs defined.
    Time for finding SS restraints: 1.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 25
      removed outlier: 3.651A  pdb=" N   ARG A  17 " --> pdb=" O   PHE A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 41
    Processing helix  chain 'A' and resid 44 through 51
    Processing helix  chain 'A' and resid 57 through 68
      Proline residue:  A  65  - end of helix
      removed outlier: 3.896A  pdb=" N   THR A  68 " --> pdb=" O   GLN A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 102
    Processing helix  chain 'A' and resid 321 through 338
      removed outlier: 3.752A  pdb=" N   PHE A 325 " --> pdb=" O   GLN A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 347
      removed outlier: 3.785A  pdb=" N   LEU A 346 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 369
    Processing helix  chain 'A' and resid 380 through 382
      No H-bonds generated for 'chain 'A' and resid 380 through 382'
    Processing helix  chain 'A' and resid 383 through 406
      removed outlier: 3.700A  pdb=" N   GLU A 388 " --> pdb=" O   GLU A 384 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ILE A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL A 390 " --> pdb=" O   GLY A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 429
      removed outlier: 3.656A  pdb=" N   THR A 427 " --> pdb=" O   GLN A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 481
    Processing helix  chain 'A' and resid 485 through 505
      removed outlier: 3.696A  pdb=" N   ASN A 489 " --> pdb=" O   TYR A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 538
    Processing helix  chain 'A' and resid 550 through 567
    Processing helix  chain 'A' and resid 570 through 585
      removed outlier: 3.519A  pdb=" N   GLN A 574 " --> pdb=" O   TYR A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 605
      removed outlier: 3.969A  pdb=" N   LEU A 593 " --> pdb=" O   SER A 589 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLN A 603 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   THR A 604 " --> pdb=" O   LYS A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 637
    Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285
      removed outlier: 6.389A  pdb=" N   LEU A 349 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ASP A 378 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASN A 351 " --> pdb=" O   CYS A 376 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   LEU A 371 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 295
    Processing sheet with id=AA3, first strand: chain 'A' and resid 471 through 475
      removed outlier: 3.665A  pdb=" N   ALA A 473 " --> pdb=" O   VAL A 463 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   SER A 445 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      removed outlier: 5.706A  pdb=" N   SER A 542 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ILE A 447 " --> pdb=" O   SER A 542 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   VAL A 544 " --> pdb=" O   ILE A 447 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   VAL A 449 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL A 607 " --> pdb=" O   GLY A 541 " (cutoff:3.500A)

    215 hydrogen bonds defined for protein.
    630 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      203 hydrogen bonds
      380 hydrogen bond angles
      0 basepair planarities
      80 basepair parallelities
      151 stacking parallelities
  Total time for adding SS restraints: 1.91

  Time building geometry restraints manager: 1.09 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: 1456
        1.33 -     1.45: 3855
        1.45 -     1.57: 3931
        1.57 -     1.69: 511
        1.69 -     1.81: 18
  Bond restraints: 9771
  Sorted by residual:
  bond pdb=" O5'   G B  57 "
       pdb=" C5'   G B  57 "
    ideal  model  delta    sigma   weight residual
    1.420  1.454 -0.034 1.50e-02 4.44e+03 5.25e+00
  bond pdb=" P     G B 224 "
       pdb=" OP2   G B 224 "
    ideal  model  delta    sigma   weight residual
    1.485  1.524 -0.039 2.00e-02 2.50e+03 3.87e+00
  bond pdb=" O5'   G B 224 "
       pdb=" C5'   G B 224 "
    ideal  model  delta    sigma   weight residual
    1.420  1.449 -0.029 1.50e-02 4.44e+03 3.83e+00
  bond pdb=" O5'   G B  56 "
       pdb=" C5'   G B  56 "
    ideal  model  delta    sigma   weight residual
    1.424  1.453 -0.029 1.50e-02 4.44e+03 3.77e+00
  bond pdb=" P     G B  56 "
       pdb=" OP2   G B  56 "
    ideal  model  delta    sigma   weight residual
    1.485  1.523 -0.038 2.00e-02 2.50e+03 3.69e+00
  ... (remaining 9766 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 14131
        1.64 -     3.28: 254
        3.28 -     4.91: 58
        4.91 -     6.55: 10
        6.55 -     8.19: 6
  Bond angle restraints: 14459
  Sorted by residual:
  angle pdb=" O3'   G B  56 "
        pdb=" C3'   G B  56 "
        pdb=" C2'   G B  56 "
      ideal   model   delta    sigma   weight residual
     109.50  116.76   -7.26 1.50e+00 4.44e-01 2.34e+01
  angle pdb=" O3'   G B 189 "
        pdb=" C3'   G B 189 "
        pdb=" C2'   G B 189 "
      ideal   model   delta    sigma   weight residual
     109.50  116.52   -7.02 1.50e+00 4.44e-01 2.19e+01
  angle pdb=" C4'   G B  56 "
        pdb=" C3'   G B  56 "
        pdb=" O3'   G B  56 "
      ideal   model   delta    sigma   weight residual
     109.40  115.70   -6.30 1.50e+00 4.44e-01 1.76e+01
  angle pdb=" C4'   G B 189 "
        pdb=" C3'   G B 189 "
        pdb=" O3'   G B 189 "
      ideal   model   delta    sigma   weight residual
     109.40  114.53   -5.13 1.50e+00 4.44e-01 1.17e+01
  angle pdb=" N   GLY A 569 "
        pdb=" CA  GLY A 569 "
        pdb=" C   GLY A 569 "
      ideal   model   delta    sigma   weight residual
     113.18  120.19   -7.01 2.37e+00 1.78e-01 8.75e+00
  ... (remaining 14454 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.08: 5286
       35.08 -    70.15: 688
       70.15 -   105.23: 69
      105.23 -   140.30: 2
      140.30 -   175.38: 11
  Dihedral angle restraints: 6056
    sinusoidal: 4733
      harmonic: 1323
  Sorted by residual:
  dihedral pdb=" C4'   G B 189 "
           pdb=" C3'   G B 189 "
           pdb=" C2'   G B 189 "
           pdb=" C1'   G B 189 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   32.64  -67.64     1      8.00e+00 1.56e-02 9.29e+01
  dihedral pdb=" C5'   G B 189 "
           pdb=" C4'   G B 189 "
           pdb=" C3'   G B 189 "
           pdb=" O3'   G B 189 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   79.79   67.21     1      8.00e+00 1.56e-02 9.19e+01
  dihedral pdb=" O4'   C B 196 "
           pdb=" C1'   C B 196 "
           pdb=" N1    C B 196 "
           pdb=" C2    C B 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   26.02  173.98     1      1.50e+01 4.44e-03 8.51e+01
  ... (remaining 6053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 1753
       0.083 -    0.165: 54
       0.165 -    0.248: 7
       0.248 -    0.330: 3
       0.330 -    0.413: 2
  Chirality restraints: 1819
  Sorted by residual:
  chirality pdb=" C3'   G B 189 "
            pdb=" C4'   G B 189 "
            pdb=" O3'   G B 189 "
            pdb=" C2'   G B 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.33   -0.41 2.00e-01 2.50e+01 4.27e+00
  chirality pdb=" C3'   G B  56 "
            pdb=" C4'   G B  56 "
            pdb=" O3'   G B  56 "
            pdb=" C2'   G B  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.34   -0.40 2.00e-01 2.50e+01 4.10e+00
  chirality pdb=" P     G B  57 "
            pdb=" OP1   G B  57 "
            pdb=" OP2   G B  57 "
            pdb=" O5'   G B  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.72   -0.31 2.00e-01 2.50e+01 2.44e+00
  ... (remaining 1816 not shown)

  Planarity restraints: 887
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  96 "    0.025 2.00e-02 2.50e+03   1.54e-02 5.33e+00
        pdb=" N1    C B  96 "   -0.032 2.00e-02 2.50e+03
        pdb=" C2    C B  96 "    0.004 2.00e-02 2.50e+03
        pdb=" O2    C B  96 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3    C B  96 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    C B  96 "    0.020 2.00e-02 2.50e+03
        pdb=" N4    C B  96 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    C B  96 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C B  96 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  97 "    0.030 2.00e-02 2.50e+03   1.51e-02 5.16e+00
        pdb=" N1    C B  97 "   -0.030 2.00e-02 2.50e+03
        pdb=" C2    C B  97 "   -0.006 2.00e-02 2.50e+03
        pdb=" O2    C B  97 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    C B  97 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    C B  97 "    0.007 2.00e-02 2.50e+03
        pdb=" N4    C B  97 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    C B  97 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    C B  97 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B  45 "    0.029 2.00e-02 2.50e+03   1.46e-02 4.81e+00
        pdb=" N1    U B  45 "   -0.030 2.00e-02 2.50e+03
        pdb=" C2    U B  45 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2    U B  45 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    U B  45 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    U B  45 "    0.004 2.00e-02 2.50e+03
        pdb=" O4    U B  45 "    0.008 2.00e-02 2.50e+03
        pdb=" C5    U B  45 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    U B  45 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 884 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1338
        2.76 -     3.29: 8146
        3.29 -     3.83: 18195
        3.83 -     4.36: 20224
        4.36 -     4.90: 28501
  Nonbonded interactions: 76404
  Sorted by model distance:
  nonbonded pdb=" O6    G B 165 "
            pdb=" O4    U B 173 "
     model   vdw
     2.224 2.432
  nonbonded pdb=" O2'   G B 189 "
            pdb=" O5'   A B 190 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O2'   A B 190 "
            pdb=" O4'   A B 191 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O2    U B  30 "
            pdb=" N1    G B  31 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" ND2 ASN A 379 "
            pdb=" OE1 GLN A 603 "
     model   vdw
     2.294 3.120
  ... (remaining 76399 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
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   0.039   9771  Z= 0.143
  Angle     :  0.580   8.191  14459  Z= 0.308
  Chirality :  0.037   0.413   1819
  Planarity :  0.003   0.047    887
  Dihedral  : 24.550 175.377   5198
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  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:  1.68 (0.40), residues: 446
  helix:  2.21 (0.33), residues: 244
  sheet: -0.00 (0.61), residues: 67
  loop : -0.27 (0.55), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A 327 
 TYR   0.013   0.001   TYR A 570 
 PHE   0.012   0.002   PHE A 325 
 TRP   0.009   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9771)
  covalent geometry    : angle       0.57956 (14459)
  hydrogen bonds       : bond        0.10406 (  418)
  hydrogen bonds       : angle       4.34532 ( 1010)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.176 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0738
  time to fit residues: 6.8172
Evaluate side-chains
  47 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:   30.0000
   chunk 45 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    5.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 489 ASN
A 496 GLN
A 586 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.131192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.091147 restraints weight = 22023.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.093955 restraints weight = 8878.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.095707 restraints weight = 5820.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.096557 restraints weight = 4840.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.096712 restraints weight = 4473.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.051   9771  Z= 0.420
  Angle     :  0.807   8.120  14459  Z= 0.419
  Chirality :  0.045   0.309   1819
  Planarity :  0.006   0.071    887
  Dihedral  : 25.578 176.967   4362
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 11.08 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.95 (0.39), residues: 446
  helix:  1.69 (0.33), residues: 246
  sheet: -0.15 (0.65), residues: 64
  loop : -0.90 (0.50), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  17 
 TYR   0.016   0.003   TYR A  80 
 PHE   0.019   0.003   PHE A 347 
 TRP   0.011   0.002   TRP A 382 
 HIS   0.005   0.002   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00859 ( 9771)
  covalent geometry    : angle       0.80656 (14459)
  hydrogen bonds       : bond        0.06600 (  418)
  hydrogen bonds       : angle       3.98415 ( 1010)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A   81 MET cc_start: 0.8117 (tpp) cc_final: 0.7901 (tpp)
REVERT: A  310 ASP cc_start: 0.8560 (p0) cc_final: 0.8271 (p0)
REVERT: A  441 TYR cc_start: 0.8436 (t80) cc_final: 0.8207 (t80)
  outliers start: 11
  outliers final: 3
  residues processed: 51
  average time/residue: 0.0565
  time to fit residues: 4.8703
Evaluate side-chains
  42 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  626 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0870
   chunk 4 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 60 optimal weight:   50.0000
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.133211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.093805 restraints weight = 21111.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.096575 restraints weight = 8948.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 70)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.098288 restraints weight = 5966.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.099161 restraints weight = 4969.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.099325 restraints weight = 4578.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9771  Z= 0.148
  Angle     :  0.564   7.685  14459  Z= 0.297
  Chirality :  0.034   0.229   1819
  Planarity :  0.004   0.053    887
  Dihedral  : 25.314 179.666   4362
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.78 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.38 (0.40), residues: 446
  helix:  2.08 (0.33), residues: 246
  sheet: -0.05 (0.66), residues: 63
  loop : -0.73 (0.52), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  17 
 TYR   0.010   0.001   TYR A 374 
 PHE   0.010   0.002   PHE A 281 
 TRP   0.005   0.001   TRP A 382 
 HIS   0.003   0.001   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9771)
  covalent geometry    : angle       0.56351 (14459)
  hydrogen bonds       : bond        0.05204 (  418)
  hydrogen bonds       : angle       3.37701 ( 1010)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A  273 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7962 (pp)
  outliers start: 6
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0648
  time to fit residues: 5.4370
Evaluate side-chains
  49 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  626 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    0.4980
   chunk 48 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 59 optimal weight:   30.0000
   chunk 46 optimal weight:    7.9990
   chunk 60 optimal weight:   50.0000
   chunk 36 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    2.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.131279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.091868 restraints weight = 21287.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.094595 restraints weight = 8916.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.096263 restraints weight = 5892.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.097120 restraints weight = 4895.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.097485 restraints weight = 4510.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9771  Z= 0.208
  Angle     :  0.588   8.856  14459  Z= 0.310
  Chirality :  0.035   0.225   1819
  Planarity :  0.004   0.043    887
  Dihedral  : 25.301 179.544   4362
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 13.51 %
    Favored  : 82.97 %
  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:  1.34 (0.40), residues: 446
  helix:  2.07 (0.33), residues: 246
  sheet: -0.10 (0.64), residues: 64
  loop : -0.78 (0.51), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  17 
 TYR   0.010   0.001   TYR A 570 
 PHE   0.012   0.002   PHE A 325 
 TRP   0.006   0.001   TRP A 588 
 HIS   0.004   0.001   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 9771)
  covalent geometry    : angle       0.58752 (14459)
  hydrogen bonds       : bond        0.05353 (  418)
  hydrogen bonds       : angle       3.33692 ( 1010)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   89 TYR cc_start: 0.7976 (m-10) cc_final: 0.7568 (m-10)
REVERT: A  273 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7948 (pp)
REVERT: A  461 VAL cc_start: 0.9410 (t) cc_final: 0.9168 (p)
  outliers start: 13
  outliers final: 5
  residues processed: 55
  average time/residue: 0.0677
  time to fit residues: 5.7706
Evaluate side-chains
  49 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  626 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 49 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 59 optimal weight:   30.0000
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 446 HIS
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.136299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.096709 restraints weight = 21224.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.099600 restraints weight = 8754.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.101314 restraints weight = 5754.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.102300 restraints weight = 4783.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.102489 restraints weight = 4389.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9771  Z= 0.133
  Angle     :  0.536   9.754  14459  Z= 0.282
  Chirality :  0.033   0.224   1819
  Planarity :  0.004   0.039    887
  Dihedral  : 25.157 179.693   4362
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 12.97 %
    Favored  : 82.97 %
  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:  1.59 (0.40), residues: 446
  helix:  2.31 (0.34), residues: 242
  sheet:  0.12 (0.66), residues: 64
  loop : -0.73 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 350 
 TYR   0.012   0.001   TYR A  91 
 PHE   0.010   0.002   PHE A 325 
 TRP   0.004   0.001   TRP A  21 
 HIS   0.002   0.001   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9771)
  covalent geometry    : angle       0.53630 (14459)
  hydrogen bonds       : bond        0.04918 (  418)
  hydrogen bonds       : angle       3.10813 ( 1010)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A   89 TYR cc_start: 0.7885 (m-10) cc_final: 0.7487 (m-10)
REVERT: A  273 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7983 (pp)
REVERT: A  550 ASP cc_start: 0.7991 (m-30) cc_final: 0.7778 (m-30)
  outliers start: 15
  outliers final: 10
  residues processed: 61
  average time/residue: 0.0586
  time to fit residues: 5.7098
Evaluate side-chains
  59 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  626 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 65 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 64 optimal weight:   10.0000
   chunk 40 optimal weight:    0.6980
   chunk 54 optimal weight:   20.0000
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 306 ASN
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.130647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.090750 restraints weight = 21207.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 74)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.093447 restraints weight = 9105.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.095105 restraints weight = 6079.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.095767 restraints weight = 5050.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.096385 restraints weight = 4706.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9771  Z= 0.229
  Angle     :  0.608   9.081  14459  Z= 0.317
  Chirality :  0.036   0.226   1819
  Planarity :  0.004   0.035    887
  Dihedral  : 25.189 179.226   4362
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 17.03 %
    Favored  : 79.46 %
  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:  1.40 (0.40), residues: 446
  helix:  2.21 (0.33), residues: 242
  sheet: -0.12 (0.67), residues: 64
  loop : -0.86 (0.49), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 350 
 TYR   0.011   0.002   TYR A 570 
 PHE   0.013   0.002   PHE A 305 
 TRP   0.007   0.001   TRP A 588 
 HIS   0.004   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 9771)
  covalent geometry    : angle       0.60763 (14459)
  hydrogen bonds       : bond        0.05327 (  418)
  hydrogen bonds       : angle       3.31663 ( 1010)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A   89 TYR cc_start: 0.7981 (m-10) cc_final: 0.7604 (m-10)
REVERT: A  273 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7987 (pp)
REVERT: A  290 ASP cc_start: 0.8023 (t0) cc_final: 0.7750 (t0)
REVERT: A  461 VAL cc_start: 0.9429 (t) cc_final: 0.9204 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 53
  average time/residue: 0.0634
  time to fit residues: 5.5347
Evaluate side-chains
  52 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  626 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 64 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 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 = 0.3976 r_free = 0.3976 target = 0.135327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.096323 restraints weight = 21279.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.099145 restraints weight = 8948.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.100914 restraints weight = 5914.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.101743 restraints weight = 4893.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.102237 restraints weight = 4509.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9771  Z= 0.115
  Angle     :  0.537  10.121  14459  Z= 0.279
  Chirality :  0.033   0.226   1819
  Planarity :  0.004   0.033    887
  Dihedral  : 25.035 179.487   4362
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.84 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.62 (0.41), residues: 446
  helix:  2.45 (0.34), residues: 242
  sheet: -0.20 (0.67), residues: 63
  loop : -0.78 (0.50), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  17 
 TYR   0.011   0.001   TYR A  91 
 PHE   0.009   0.002   PHE A 325 
 TRP   0.004   0.001   TRP A  21 
 HIS   0.002   0.000   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 9771)
  covalent geometry    : angle       0.53704 (14459)
  hydrogen bonds       : bond        0.04732 (  418)
  hydrogen bonds       : angle       3.00943 ( 1010)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A   89 TYR cc_start: 0.7838 (m-10) cc_final: 0.7470 (m-10)
REVERT: A  273 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8057 (pp)
REVERT: A  290 ASP cc_start: 0.8045 (t0) cc_final: 0.7742 (t0)
  outliers start: 11
  outliers final: 8
  residues processed: 60
  average time/residue: 0.0642
  time to fit residues: 6.0583
Evaluate side-chains
  61 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  626 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 10 optimal weight:    0.0070
   chunk 7 optimal weight:    0.0060
   chunk 29 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 61 optimal weight:   30.0000
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.9418

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 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 = 0.3981 r_free = 0.3981 target = 0.135772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.096985 restraints weight = 21148.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.099817 restraints weight = 8830.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.101562 restraints weight = 5793.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.102456 restraints weight = 4793.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.102562 restraints weight = 4408.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9771  Z= 0.113
  Angle     :  0.532  10.228  14459  Z= 0.277
  Chirality :  0.032   0.222   1819
  Planarity :  0.003   0.033    887
  Dihedral  : 24.961 179.392   4362
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.19 %
    Favored  : 77.84 %
  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:  1.72 (0.41), residues: 446
  helix:  2.54 (0.33), residues: 242
  sheet: -0.16 (0.67), residues: 63
  loop : -0.73 (0.50), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 275 
 TYR   0.018   0.001   TYR A  91 
 PHE   0.009   0.001   PHE A 325 
 TRP   0.004   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 9771)
  covalent geometry    : angle       0.53200 (14459)
  hydrogen bonds       : bond        0.04618 (  418)
  hydrogen bonds       : angle       3.00945 ( 1010)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   89 TYR cc_start: 0.7802 (m-10) cc_final: 0.7395 (m-10)
REVERT: A  273 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8059 (pp)
REVERT: A  290 ASP cc_start: 0.8149 (t0) cc_final: 0.7464 (t0)
  outliers start: 11
  outliers final: 9
  residues processed: 58
  average time/residue: 0.0549
  time to fit residues: 5.2119
Evaluate side-chains
  58 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  626 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 59 optimal weight:   30.0000
   chunk 33 optimal weight:    8.9990
   chunk 60 optimal weight:   50.0000
   chunk 47 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 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 = 0.3853 r_free = 0.3853 target = 0.126474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.086366 restraints weight = 21164.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.088900 restraints weight = 9298.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.090518 restraints weight = 6269.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.091368 restraints weight = 5236.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.091572 restraints weight = 4817.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.063   9771  Z= 0.422
  Angle     :  0.807   9.214  14459  Z= 0.414
  Chirality :  0.045   0.256   1819
  Planarity :  0.005   0.046    887
  Dihedral  : 25.478 177.814   4362
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 19.19 %
    Favored  : 77.03 %
  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:  0.84 (0.39), residues: 446
  helix:  1.67 (0.32), residues: 246
  sheet: -0.16 (0.69), residues: 64
  loop : -1.12 (0.49), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 525 
 TYR   0.020   0.003   TYR A 441 
 PHE   0.021   0.003   PHE A 305 
 TRP   0.010   0.002   TRP A  21 
 HIS   0.006   0.002   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00865 ( 9771)
  covalent geometry    : angle       0.80697 (14459)
  hydrogen bonds       : bond        0.06536 (  418)
  hydrogen bonds       : angle       3.88668 ( 1010)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A  273 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8084 (pp)
REVERT: A  290 ASP cc_start: 0.7966 (t0) cc_final: 0.7619 (t0)
REVERT: A  310 ASP cc_start: 0.8439 (p0) cc_final: 0.8202 (p0)
  outliers start: 14
  outliers final: 7
  residues processed: 52
  average time/residue: 0.0535
  time to fit residues: 4.7318
Evaluate side-chains
  49 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  626 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 46 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.128875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.089001 restraints weight = 21231.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.091654 restraints weight = 9277.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.093296 restraints weight = 6255.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.094117 restraints weight = 5230.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.094204 restraints weight = 4827.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9771  Z= 0.248
  Angle     :  0.645   8.758  14459  Z= 0.335
  Chirality :  0.038   0.236   1819
  Planarity :  0.004   0.040    887
  Dihedral  : 25.365 179.339   4362
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.27 %
    Favored  : 77.30 %
  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:  1.10 (0.40), residues: 446
  helix:  2.01 (0.33), residues: 242
  sheet: -0.16 (0.68), residues: 64
  loop : -1.12 (0.48), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 475 
 TYR   0.014   0.002   TYR A 441 
 PHE   0.015   0.002   PHE A 305 
 TRP   0.003   0.001   TRP A 588 
 HIS   0.003   0.001   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 9771)
  covalent geometry    : angle       0.64520 (14459)
  hydrogen bonds       : bond        0.05368 (  418)
  hydrogen bonds       : angle       3.44193 ( 1010)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  273 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8110 (pp)
REVERT: A  290 ASP cc_start: 0.7961 (t0) cc_final: 0.7619 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 51
  average time/residue: 0.0513
  time to fit residues: 4.4589
Evaluate side-chains
  49 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  626 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 57 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.132906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.093839 restraints weight = 20795.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.096548 restraints weight = 8846.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.098268 restraints weight = 5878.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.098943 restraints weight = 4885.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.099492 restraints weight = 4539.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9771  Z= 0.144
  Angle     :  0.570   9.493  14459  Z= 0.296
  Chirality :  0.034   0.229   1819
  Planarity :  0.004   0.034    887
  Dihedral  : 25.167 179.978   4362
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 21.08 %
    Favored  : 77.03 %
  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:  1.43 (0.41), residues: 446
  helix:  2.28 (0.34), residues: 242
  sheet: -0.10 (0.68), residues: 64
  loop : -0.94 (0.49), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  17 
 TYR   0.021   0.002   TYR A  91 
 PHE   0.011   0.002   PHE A 305 
 TRP   0.004   0.001   TRP A 366 
 HIS   0.003   0.001   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9771)
  covalent geometry    : angle       0.56967 (14459)
  hydrogen bonds       : bond        0.04726 (  418)
  hydrogen bonds       : angle       3.16821 ( 1010)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1545.06 seconds
wall clock time: 27 minutes 18.01 seconds (1638.01 seconds total)