Starting phenix.real_space_refine
on Fri Aug 22 12:40:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ta6_41130/08_2025/8ta6_41130.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ta6_41130/08_2025/8ta6_41130.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ta6_41130/08_2025/8ta6_41130.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ta6_41130/08_2025/8ta6_41130.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ta6_41130/08_2025/8ta6_41130.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ta6_41130/08_2025/8ta6_41130.map"
  }
  resolution = 4.03
  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=   0.000 sd=   0.051
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: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1368      2.51       5
     N     400      2.21       5
     O     380      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2158
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1079
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 5, 'TRANS': 131}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1079
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 5, 'TRANS': 131}
          Chain breaks: 1
  Time building chain proxies: 1.31, per 1000 atoms: 0.61
  Number of scatterers: 2158
  At special positions: 0
  Unit cell: (75.68, 70.004, 80.41, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     380      8.00
     N     400      7.00
     C    1368      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: 0.24
  Conformation dependent library (CDL) restraints added in 94.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  512

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 4 sheets defined
      36.9% alpha, 13.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 573 through 578
    Processing helix  chain 'A' and resid 579 through 583
    Processing helix  chain 'A' and resid 596 through 607
      removed outlier: 3.648A  pdb=" N   LEU A 600 " --> pdb=" O   THR A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 641
    Processing helix  chain 'A' and resid 784 through 788
    Processing helix  chain 'A' and resid 802 through 811
      removed outlier: 4.575A  pdb=" N   THR A 808 " --> pdb=" O   HIS A 804 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE A 810 " --> pdb=" O   THR A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 841
    Processing helix  chain 'B' and resid 599 through 604
      removed outlier: 3.795A  pdb=" N   ALA B 603 " --> pdb=" O   ASP B 599 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU B 604 " --> pdb=" O   LEU B 600 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 599 through 604'
    Processing helix  chain 'B' and resid 628 through 640
      removed outlier: 3.570A  pdb=" N   VAL B 632 " --> pdb=" O   GLU B 628 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA B 634 " --> pdb=" O   SER B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 802 through 814
      removed outlier: 3.513A  pdb=" N   THR B 806 " --> pdb=" O   SER B 802 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU B 813 " --> pdb=" O   ILE B 809 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 832 through 839
    Processing sheet with id=AA1, first strand: chain 'A' and resid 590 through 592
      removed outlier: 6.330A  pdb=" N   VAL A 591 " --> pdb=" O   VAL A 615 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   LEU A 612 " --> pdb=" O   SER A 626 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 612 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   LEU A 614 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 796 through 798
      removed outlier: 5.908A  pdb=" N   LEU A 797 " --> pdb=" O   THR A 821 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLY A 828 " --> pdb=" O   VAL A 820 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   SER A 822 " --> pdb=" O   LEU A 826 " (cutoff:3.500A)
      removed outlier: 5.285A  pdb=" N   LEU A 826 " --> pdb=" O   SER A 822 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 590 through 592
      removed outlier: 6.736A  pdb=" N   VAL B 591 " --> pdb=" O   VAL B 615 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY B 625 " --> pdb=" O   LEU B 614 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 796 through 797
      removed outlier: 3.840A  pdb=" N   GLY B 828 " --> pdb=" O   VAL B 820 " (cutoff:3.500A)

    60 hydrogen bonds defined for protein.
    159 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.26

  Time building geometry restraints manager: 0.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 640
        1.34 -     1.46: 283
        1.46 -     1.58: 1253
        1.58 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 2192
  Sorted by residual:
  bond pdb=" CA  ASP A 791 "
       pdb=" C   ASP A 791 "
    ideal  model  delta    sigma   weight residual
    1.524  1.556 -0.032 1.26e-02 6.30e+03 6.44e+00
  bond pdb=" CZ  ARG B 629 "
       pdb=" NH2 ARG B 629 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.29e+00
  bond pdb=" CZ  ARG A 629 "
       pdb=" NH2 ARG A 629 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.25e+00
  bond pdb=" CD2 HIS A 804 "
       pdb=" NE2 HIS A 804 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.20e+00
  bond pdb=" CZ  ARG B 577 "
       pdb=" NH2 ARG B 577 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.17e+00
  ... (remaining 2187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 1943
        1.75 -     3.50: 777
        3.50 -     5.24: 196
        5.24 -     6.99: 37
        6.99 -     8.74: 5
  Bond angle restraints: 2958
  Sorted by residual:
  angle pdb=" CA  ASP A 787 "
        pdb=" CB  ASP A 787 "
        pdb=" CG  ASP A 787 "
      ideal   model   delta    sigma   weight residual
     112.60  117.96   -5.36 1.00e+00 1.00e+00 2.87e+01
  angle pdb=" C   MET A 584 "
        pdb=" N   VAL A 585 "
        pdb=" CA  VAL A 585 "
      ideal   model   delta    sigma   weight residual
     120.98  128.03   -7.05 1.36e+00 5.41e-01 2.69e+01
  angle pdb=" N   MET A 611 "
        pdb=" CA  MET A 611 "
        pdb=" C   MET A 611 "
      ideal   model   delta    sigma   weight residual
     108.99  116.66   -7.67 1.57e+00 4.06e-01 2.39e+01
  angle pdb=" OE1 GLN B 639 "
        pdb=" CD  GLN B 639 "
        pdb=" NE2 GLN B 639 "
      ideal   model   delta    sigma   weight residual
     122.60  117.77    4.83 1.00e+00 1.00e+00 2.34e+01
  angle pdb=" N   GLY B 571 "
        pdb=" CA  GLY B 571 "
        pdb=" C   GLY B 571 "
      ideal   model   delta    sigma   weight residual
     111.21  116.18   -4.97 1.04e+00 9.25e-01 2.28e+01
  ... (remaining 2953 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 1196
       17.58 -    35.16: 116
       35.16 -    52.74: 17
       52.74 -    70.31: 5
       70.31 -    87.89: 4
  Dihedral angle restraints: 1338
    sinusoidal: 552
      harmonic: 786
  Sorted by residual:
  dihedral pdb=" CA  ARG A 572 "
           pdb=" C   ARG A 572 "
           pdb=" N   HIS A 573 "
           pdb=" CA  HIS A 573 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.45  -29.55     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  VAL B 585 "
           pdb=" C   VAL B 585 "
           pdb=" N   ARG B 586 "
           pdb=" CA  ARG B 586 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.13  -28.87     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  ARG A 610 "
           pdb=" C   ARG A 610 "
           pdb=" N   MET A 611 "
           pdb=" CA  MET A 611 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.24  -26.76     0      5.00e+00 4.00e-02 2.86e+01
  ... (remaining 1335 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 174
       0.072 -    0.143: 120
       0.143 -    0.214: 46
       0.214 -    0.285: 11
       0.285 -    0.357: 1
  Chirality restraints: 352
  Sorted by residual:
  chirality pdb=" CA  MET B 621 "
            pdb=" N   MET B 621 "
            pdb=" C   MET B 621 "
            pdb=" CB  MET B 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.18e+00
  chirality pdb=" CA  GLN A 575 "
            pdb=" N   GLN A 575 "
            pdb=" C   GLN A 575 "
            pdb=" CB  GLN A 575 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CA  MET A 621 "
            pdb=" N   MET A 621 "
            pdb=" C   MET A 621 "
            pdb=" CB  MET A 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 349 not shown)

  Planarity restraints: 372
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 785 "    0.125 2.00e-02 2.50e+03   7.65e-02 1.02e+02
        pdb=" CG  PHE A 785 "   -0.094 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 785 "   -0.073 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 785 "   -0.068 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 785 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 785 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 785 "    0.076 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 570 "    0.096 2.00e-02 2.50e+03   4.79e-02 5.72e+01
        pdb=" CG  TRP A 570 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 570 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 570 "   -0.044 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 570 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 570 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 570 "   -0.072 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 570 "    0.043 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 570 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 570 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 570 "    0.080 2.00e-02 2.50e+03   3.96e-02 3.91e+01
        pdb=" CG  TRP B 570 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 570 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 570 "   -0.034 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 570 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 570 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 570 "   -0.057 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 570 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 570 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 570 "    0.047 2.00e-02 2.50e+03
  ... (remaining 369 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     3.00: 992
        3.00 -     3.47: 2273
        3.47 -     3.95: 3209
        3.95 -     4.42: 3182
        4.42 -     4.90: 5389
  Nonbonded interactions: 15045
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 628 "
            pdb=" OG  SER A 630 "
     model   vdw
     2.524 3.040
  nonbonded pdb=" OE1 GLU B 616 "
            pdb=" OG  SER B 620 "
     model   vdw
     2.543 3.040
  nonbonded pdb=" OG  SER A 617 "
            pdb=" OE2 GLU A 619 "
     model   vdw
     2.547 3.040
  nonbonded pdb=" OG1 THR B 831 "
            pdb=" OE1 GLU B 834 "
     model   vdw
     2.560 3.040
  nonbonded pdb=" N   SER A 822 "
            pdb=" O   SER A 822 "
     model   vdw
     2.579 2.496
  ... (remaining 15040 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.460
  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:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.110
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
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      :  0.013   0.039   2192  Z= 0.806
  Angle     :  1.987   8.737   2958  Z= 1.304
  Chirality :  0.103   0.357    352
  Planarity :  0.014   0.087    372
  Dihedral  : 15.103  87.892    826
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 0.91
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  9.40 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.13 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.39 %
  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 aren not related in a simple way.
  whole: -2.23 (0.49), residues: 266
  helix: -2.32 (0.45), residues: 76
  sheet: -2.24 (0.97), residues: 22
  loop : -0.90 (0.50), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 836 
 TYR   0.052   0.021   TYR A 819 
 PHE   0.125   0.019   PHE A 785 
 TRP   0.096   0.036   TRP A 570 
 HIS   0.006   0.002   HIS B 590 

Details of bonding type rmsd
  covalent geometry    : bond        0.01253 ( 2192)
  covalent geometry    : angle       1.98691 ( 2958)
  hydrogen bonds       : bond        0.18374 (   60)
  hydrogen bonds       : angle       7.86426 (  159)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.9622 (p-80) cc_final: 0.9188 (p-80)
REVERT: A  611 MET cc_start: 0.8216 (tpp) cc_final: 0.7962 (tpp)
REVERT: A  836 ARG cc_start: 0.6537 (mmt180) cc_final: 0.5747 (mpt180)
REVERT: B  577 ARG cc_start: 0.8577 (ttp80) cc_final: 0.7928 (mmt180)
REVERT: B  581 GLU cc_start: 0.8586 (tt0) cc_final: 0.8386 (tt0)
REVERT: B  582 ASP cc_start: 0.8170 (m-30) cc_final: 0.7785 (m-30)
REVERT: B  607 THR cc_start: 0.9365 (p) cc_final: 0.8966 (p)
REVERT: B  629 ARG cc_start: 0.7950 (mtt180) cc_final: 0.5543 (ptm160)
REVERT: B  785 PHE cc_start: 0.8708 (p90) cc_final: 0.8475 (p90)
REVERT: B  834 GLU cc_start: 0.9537 (mp0) cc_final: 0.9121 (mp0)
  outliers start: 5
  outliers final: 1
  residues processed: 72
  average time/residue: 0.1134
  time to fit residues: 8.9537
Evaluate side-chains
  49 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.152826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.134820 restraints weight = 5531.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.137930 restraints weight = 3337.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.140000 restraints weight = 2264.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.141555 restraints weight = 1688.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.142683 restraints weight = 1329.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2192  Z= 0.150
  Angle     :  0.718   5.254   2958  Z= 0.385
  Chirality :  0.046   0.138    352
  Planarity :  0.005   0.041    372
  Dihedral  :  7.103  23.794    300
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  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 aren not related in a simple way.
  whole: -1.81 (0.51), residues: 266
  helix: -1.07 (0.54), residues: 79
  sheet: -1.47 (0.80), residues: 40
  loop : -1.12 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 825 
 TYR   0.007   0.002   TYR A 819 
 PHE   0.014   0.002   PHE A 810 
 TRP   0.017   0.002   TRP A 570 
 HIS   0.004   0.001   HIS A 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 2192)
  covalent geometry    : angle       0.71792 ( 2958)
  hydrogen bonds       : bond        0.04192 (   60)
  hydrogen bonds       : angle       5.23817 (  159)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  584 MET cc_start: 0.2716 (tpt) cc_final: 0.2449 (tpt)
REVERT: A  590 HIS cc_start: 0.8340 (p-80) cc_final: 0.7949 (p-80)
REVERT: A  784 ASN cc_start: 0.8581 (t0) cc_final: 0.8245 (t0)
REVERT: A  836 ARG cc_start: 0.5241 (mmt180) cc_final: 0.4869 (mpt180)
REVERT: B  607 THR cc_start: 0.8841 (p) cc_final: 0.8292 (p)
REVERT: B  629 ARG cc_start: 0.6504 (mtt180) cc_final: 0.5136 (ttm-80)
REVERT: B  834 GLU cc_start: 0.8829 (mp0) cc_final: 0.8595 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1207
  time to fit residues: 8.7851
Evaluate side-chains
  46 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0040
   chunk 8 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.7596

-------------------------------------------------------------------------------
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 = 0.4125 r_free = 0.4125 target = 0.153413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.135525 restraints weight = 5480.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.138615 restraints weight = 3207.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.140707 restraints weight = 2146.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.142253 restraints weight = 1581.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.143325 restraints weight = 1247.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2192  Z= 0.116
  Angle     :  0.638   5.442   2958  Z= 0.335
  Chirality :  0.043   0.133    352
  Planarity :  0.004   0.043    372
  Dihedral  :  6.108  20.473    300
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  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 aren not related in a simple way.
  whole: -1.41 (0.51), residues: 266
  helix: -0.39 (0.59), residues: 80
  sheet: -1.04 (0.87), residues: 35
  loop : -1.18 (0.51), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 610 
 TYR   0.004   0.001   TYR B 819 
 PHE   0.010   0.002   PHE A 810 
 TRP   0.011   0.002   TRP A 570 
 HIS   0.009   0.001   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 2192)
  covalent geometry    : angle       0.63761 ( 2958)
  hydrogen bonds       : bond        0.03406 (   60)
  hydrogen bonds       : angle       4.85319 (  159)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  584 MET cc_start: 0.2835 (tpt) cc_final: 0.2577 (tpt)
REVERT: A  590 HIS cc_start: 0.8355 (p-80) cc_final: 0.7958 (p-80)
REVERT: A  622 ILE cc_start: 0.8529 (mt) cc_final: 0.8246 (mt)
REVERT: A  784 ASN cc_start: 0.8621 (t0) cc_final: 0.8226 (t0)
REVERT: B  607 THR cc_start: 0.8804 (p) cc_final: 0.8292 (p)
REVERT: B  629 ARG cc_start: 0.6459 (mtt180) cc_final: 0.5077 (ttm-80)
REVERT: B  834 GLU cc_start: 0.8770 (mp0) cc_final: 0.8535 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1203
  time to fit residues: 8.6403
Evaluate side-chains
  44 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 8 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.4150 r_free = 0.4150 target = 0.154199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.135803 restraints weight = 5986.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.138733 restraints weight = 3713.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.140762 restraints weight = 2608.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.142233 restraints weight = 1985.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.143072 restraints weight = 1607.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.4272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2192  Z= 0.118
  Angle     :  0.608   5.212   2958  Z= 0.318
  Chirality :  0.042   0.129    352
  Planarity :  0.004   0.041    372
  Dihedral  :  5.692  19.665    300
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  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 aren not related in a simple way.
  whole: -1.29 (0.50), residues: 266
  helix: -0.17 (0.60), residues: 78
  sheet: -1.26 (0.94), residues: 25
  loop : -1.14 (0.49), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 579 
 TYR   0.010   0.002   TYR B 819 
 PHE   0.008   0.001   PHE A 810 
 TRP   0.011   0.002   TRP A 570 
 HIS   0.003   0.001   HIS B 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 2192)
  covalent geometry    : angle       0.60810 ( 2958)
  hydrogen bonds       : bond        0.03282 (   60)
  hydrogen bonds       : angle       4.80174 (  159)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8291 (p-80) cc_final: 0.7915 (p-80)
REVERT: A  784 ASN cc_start: 0.8678 (t0) cc_final: 0.8289 (t0)
REVERT: B  629 ARG cc_start: 0.6466 (mtt180) cc_final: 0.5228 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0981
  time to fit residues: 6.7644
Evaluate side-chains
  44 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0470
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    2.1684

-------------------------------------------------------------------------------
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 = 0.4103 r_free = 0.4103 target = 0.150248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.131695 restraints weight = 6132.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.134523 restraints weight = 3870.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.136477 restraints weight = 2751.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.137777 restraints weight = 2106.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.138886 restraints weight = 1729.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   2192  Z= 0.198
  Angle     :  0.710   6.918   2958  Z= 0.369
  Chirality :  0.045   0.164    352
  Planarity :  0.005   0.040    372
  Dihedral  :  6.044  19.894    300
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  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 aren not related in a simple way.
  whole: -1.48 (0.51), residues: 266
  helix: -0.26 (0.59), residues: 80
  sheet: -1.80 (1.25), residues: 15
  loop : -1.29 (0.48), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 579 
 TYR   0.010   0.002   TYR B 819 
 PHE   0.009   0.002   PHE A 810 
 TRP   0.015   0.003   TRP A 570 
 HIS   0.005   0.001   HIS B 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 2192)
  covalent geometry    : angle       0.71041 ( 2958)
  hydrogen bonds       : bond        0.03744 (   60)
  hydrogen bonds       : angle       4.97529 (  159)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8327 (p-80) cc_final: 0.7918 (p-80)
REVERT: A  622 ILE cc_start: 0.8425 (mt) cc_final: 0.7996 (mt)
REVERT: A  784 ASN cc_start: 0.8659 (t0) cc_final: 0.8330 (t0)
REVERT: B  629 ARG cc_start: 0.6495 (mtt180) cc_final: 0.5133 (ttm-80)
REVERT: B  820 VAL cc_start: 0.8559 (p) cc_final: 0.8302 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0883
  time to fit residues: 4.6928
Evaluate side-chains
  37 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 2 optimal weight:    0.3980
   chunk 16 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.4148 r_free = 0.4148 target = 0.154755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.136436 restraints weight = 5877.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.139329 restraints weight = 3747.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.141407 restraints weight = 2667.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.142846 restraints weight = 2044.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.143655 restraints weight = 1668.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.4748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2192  Z= 0.135
  Angle     :  0.643   5.389   2958  Z= 0.335
  Chirality :  0.044   0.146    352
  Planarity :  0.004   0.037    372
  Dihedral  :  5.712  18.486    300
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  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 aren not related in a simple way.
  whole: -1.49 (0.51), residues: 266
  helix: -0.28 (0.60), residues: 80
  sheet: -1.68 (0.90), residues: 25
  loop : -1.25 (0.50), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 579 
 TYR   0.010   0.001   TYR B 819 
 PHE   0.006   0.001   PHE A 810 
 TRP   0.029   0.004   TRP A 570 
 HIS   0.003   0.001   HIS A 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 2192)
  covalent geometry    : angle       0.64283 ( 2958)
  hydrogen bonds       : bond        0.03611 (   60)
  hydrogen bonds       : angle       4.87894 (  159)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8294 (p-80) cc_final: 0.7921 (p-80)
REVERT: A  784 ASN cc_start: 0.8652 (t0) cc_final: 0.8330 (t0)
REVERT: B  629 ARG cc_start: 0.6347 (mtt180) cc_final: 0.4961 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0846
  time to fit residues: 4.9123
Evaluate side-chains
  39 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 16 optimal weight:    8.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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 = 0.4137 r_free = 0.4137 target = 0.153196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.134597 restraints weight = 5978.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.137486 restraints weight = 3767.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.139425 restraints weight = 2676.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.140864 restraints weight = 2071.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.141837 restraints weight = 1701.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.4807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2192  Z= 0.146
  Angle     :  0.661   5.689   2958  Z= 0.339
  Chirality :  0.044   0.155    352
  Planarity :  0.004   0.035    372
  Dihedral  :  5.704  18.852    300
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.52), residues: 266
  helix: -0.26 (0.59), residues: 81
  sheet: -2.36 (0.75), residues: 35
  loop : -1.12 (0.53), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 579 
 TYR   0.010   0.002   TYR B 819 
 PHE   0.007   0.002   PHE A 810 
 TRP   0.041   0.005   TRP A 570 
 HIS   0.003   0.001   HIS B 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 2192)
  covalent geometry    : angle       0.66057 ( 2958)
  hydrogen bonds       : bond        0.03410 (   60)
  hydrogen bonds       : angle       4.63139 (  159)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A  590 HIS cc_start: 0.8294 (p-80) cc_final: 0.7925 (p-80)
REVERT: A  611 MET cc_start: 0.7110 (tpp) cc_final: 0.6835 (tpp)
REVERT: A  621 MET cc_start: 0.7616 (ptp) cc_final: 0.7316 (ptm)
REVERT: A  784 ASN cc_start: 0.8642 (t0) cc_final: 0.8341 (t0)
REVERT: B  607 THR cc_start: 0.8831 (p) cc_final: 0.8477 (p)
REVERT: B  629 ARG cc_start: 0.6392 (mtt180) cc_final: 0.5009 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0909
  time to fit residues: 5.2309
Evaluate side-chains
  37 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0020
   chunk 7 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0370
   chunk 17 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    1.3270

-------------------------------------------------------------------------------
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 = 0.4148 r_free = 0.4148 target = 0.153842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.135138 restraints weight = 6020.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.138027 restraints weight = 3912.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.139956 restraints weight = 2815.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.141195 restraints weight = 2165.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.142367 restraints weight = 1796.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.5086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2192  Z= 0.138
  Angle     :  0.655   5.655   2958  Z= 0.340
  Chirality :  0.044   0.151    352
  Planarity :  0.004   0.035    372
  Dihedral  :  5.581  19.020    300
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  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 aren not related in a simple way.
  whole: -1.44 (0.52), residues: 266
  helix: -0.01 (0.60), residues: 79
  sheet: -2.27 (0.76), residues: 35
  loop : -1.11 (0.53), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 825 
 TYR   0.010   0.001   TYR B 819 
 PHE   0.006   0.001   PHE A 810 
 TRP   0.045   0.005   TRP A 570 
 HIS   0.003   0.001   HIS B 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 2192)
  covalent geometry    : angle       0.65524 ( 2958)
  hydrogen bonds       : bond        0.03239 (   60)
  hydrogen bonds       : angle       4.82647 (  159)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8288 (p-80) cc_final: 0.7978 (p-80)
REVERT: A  784 ASN cc_start: 0.8671 (t0) cc_final: 0.8368 (t0)
REVERT: B  607 THR cc_start: 0.8836 (p) cc_final: 0.8526 (p)
REVERT: B  629 ARG cc_start: 0.6404 (mtt180) cc_final: 0.4960 (ttm-80)
REVERT: B  787 ASP cc_start: 0.7470 (p0) cc_final: 0.7109 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0655
  time to fit residues: 3.7698
Evaluate side-chains
  39 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4176 r_free = 0.4176 target = 0.156021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.137131 restraints weight = 6034.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.139982 restraints weight = 3854.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.141915 restraints weight = 2763.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.143506 restraints weight = 2155.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.143980 restraints weight = 1761.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.5226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2192  Z= 0.117
  Angle     :  0.636   5.326   2958  Z= 0.329
  Chirality :  0.045   0.240    352
  Planarity :  0.004   0.036    372
  Dihedral  :  5.339  17.996    300
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  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 aren not related in a simple way.
  whole: -1.50 (0.52), residues: 266
  helix: -0.01 (0.60), residues: 79
  sheet: -2.51 (0.73), residues: 35
  loop : -1.12 (0.52), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 825 
 TYR   0.011   0.001   TYR B 819 
 PHE   0.006   0.001   PHE A 810 
 TRP   0.039   0.004   TRP A 570 
 HIS   0.003   0.001   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 2192)
  covalent geometry    : angle       0.63646 ( 2958)
  hydrogen bonds       : bond        0.03139 (   60)
  hydrogen bonds       : angle       4.65886 (  159)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A  590 HIS cc_start: 0.8246 (p-80) cc_final: 0.7941 (p-80)
REVERT: A  784 ASN cc_start: 0.8659 (t0) cc_final: 0.8377 (t0)
REVERT: B  607 THR cc_start: 0.8834 (p) cc_final: 0.8500 (p)
REVERT: B  629 ARG cc_start: 0.6364 (mtt180) cc_final: 0.4964 (ttm-80)
REVERT: B  787 ASP cc_start: 0.7467 (p0) cc_final: 0.7149 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0674
  time to fit residues: 4.1595
Evaluate side-chains
  39 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 15 optimal weight:    0.0770
   chunk 1 optimal weight:    0.4980
   chunk 19 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    0.2980
   chunk 13 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.9742

-------------------------------------------------------------------------------
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 = 0.4168 r_free = 0.4168 target = 0.155211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.136796 restraints weight = 6102.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.139310 restraints weight = 3971.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.141157 restraints weight = 2900.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.142504 restraints weight = 2278.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.143159 restraints weight = 1893.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.5423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2192  Z= 0.124
  Angle     :  0.650   7.086   2958  Z= 0.336
  Chirality :  0.045   0.244    352
  Planarity :  0.004   0.037    372
  Dihedral  :  5.446  18.610    300
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  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 aren not related in a simple way.
  whole: -1.53 (0.52), residues: 266
  helix:  0.01 (0.61), residues: 79
  sheet: -2.50 (0.73), residues: 35
  loop : -1.18 (0.52), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 825 
 TYR   0.009   0.001   TYR B 819 
 PHE   0.006   0.001   PHE A 810 
 TRP   0.040   0.005   TRP A 570 
 HIS   0.003   0.001   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 2192)
  covalent geometry    : angle       0.64957 ( 2958)
  hydrogen bonds       : bond        0.03071 (   60)
  hydrogen bonds       : angle       4.57832 (  159)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  590 HIS cc_start: 0.8194 (p-80) cc_final: 0.7935 (p-80)
REVERT: A  784 ASN cc_start: 0.8629 (t0) cc_final: 0.8352 (t0)
REVERT: B  607 THR cc_start: 0.8884 (p) cc_final: 0.8556 (p)
REVERT: B  629 ARG cc_start: 0.6344 (mtt180) cc_final: 0.4927 (ttm-80)
REVERT: B  787 ASP cc_start: 0.7395 (p0) cc_final: 0.7064 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0600
  time to fit residues: 3.8705
Evaluate side-chains
  39 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.155977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.137000 restraints weight = 6088.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.139891 restraints weight = 3887.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.141798 restraints weight = 2744.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.143317 restraints weight = 2124.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.144124 restraints weight = 1733.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.5495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2192  Z= 0.127
  Angle     :  0.657   6.087   2958  Z= 0.341
  Chirality :  0.046   0.242    352
  Planarity :  0.004   0.037    372
  Dihedral  :  5.363  20.275    300
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 aren not related in a simple way.
  whole: -1.63 (0.51), residues: 266
  helix: -0.01 (0.61), residues: 79
  sheet: -2.72 (0.72), residues: 35
  loop : -1.23 (0.51), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 579 
 TYR   0.010   0.001   TYR B 819 
 PHE   0.006   0.001   PHE A 810 
 TRP   0.041   0.005   TRP A 570 
 HIS   0.003   0.001   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2192)
  covalent geometry    : angle       0.65665 ( 2958)
  hydrogen bonds       : bond        0.03074 (   60)
  hydrogen bonds       : angle       4.59442 (  159)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 675.75 seconds
wall clock time: 12 minutes 8.88 seconds (728.88 seconds total)