Starting phenix.real_space_refine
on Tue Feb  3 12:36:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ta6_41130/02_2026/8ta6_41130.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ta6_41130/02_2026/8ta6_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ta6_41130/02_2026/8ta6_41130.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ta6_41130/02_2026/8ta6_41130.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ta6_41130/02_2026/8ta6_41130.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ta6_41130/02_2026/8ta6_41130.cif"
  }
  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-2.0-5952/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: 0.74, per 1000 atoms: 0.34
  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: 0.10
  Conformation dependent library (CDL) restraints added in 82.8 milliseconds
  

  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: 0.09
  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: 0.31

  Time building geometry restraints manager: 0.15 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:             1.060
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.470
  Find NCS groups from input model:        0.020
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.050
-------------------------------------------------------------------------------
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 are 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  : 0.054 
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  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: 0.0689
  time to fit residues: 5.5063
Evaluate side-chains
  48 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
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 = 0.4107 r_free = 0.4107 target = 0.152908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.134939 restraints weight = 5535.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.138024 restraints weight = 3344.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.140159 restraints weight = 2271.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.141554 restraints weight = 1678.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.142691 restraints weight = 1338.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2192  Z= 0.149
  Angle     :  0.714   5.308   2958  Z= 0.383
  Chirality :  0.046   0.135    352
  Planarity :  0.005   0.041    372
  Dihedral  :  7.108  23.794    300
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.04
  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 are not related in a simple way.
  whole: -1.69 (0.51), residues: 266
  helix: -0.94 (0.56), residues: 77
  sheet: -1.49 (0.80), residues: 40
  loop : -1.05 (0.53), residues: 149

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   0.013   0.002   PHE A 785 
 TRP   0.017   0.003   TRP A 570 
 HIS   0.005   0.001   HIS A 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 2192)
  covalent geometry    : angle       0.71440 ( 2958)
  hydrogen bonds       : bond        0.04127 (   60)
  hydrogen bonds       : angle       5.20384 (  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
  67 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  584 MET cc_start: 0.2736 (tpt) cc_final: 0.2460 (tpt)
REVERT: A  590 HIS cc_start: 0.8354 (p-80) cc_final: 0.7953 (p-80)
REVERT: A  784 ASN cc_start: 0.8579 (t0) cc_final: 0.8244 (t0)
REVERT: A  836 ARG cc_start: 0.5224 (mmt180) cc_final: 0.4868 (mpt180)
REVERT: B  607 THR cc_start: 0.8854 (p) cc_final: 0.8315 (p)
REVERT: B  629 ARG cc_start: 0.6514 (mtt180) cc_final: 0.5159 (ttm-80)
REVERT: B  834 GLU cc_start: 0.8828 (mp0) cc_final: 0.8586 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0781
  time to fit residues: 5.7758
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  : 0.049 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 12 optimal weight:    0.4980
   chunk 18 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    0.1980
   chunk 7 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4143 r_free = 0.4143 target = 0.154946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.136228 restraints weight = 5473.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.139397 restraints weight = 3218.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.141564 restraints weight = 2177.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.143044 restraints weight = 1625.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.144232 restraints weight = 1295.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2192  Z= 0.110
  Angle     :  0.618   5.477   2958  Z= 0.325
  Chirality :  0.043   0.134    352
  Planarity :  0.004   0.042    372
  Dihedral  :  5.936  20.053    300
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  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 are not related in a simple way.
  whole: -1.43 (0.51), residues: 266
  helix: -0.39 (0.59), residues: 80
  sheet: -1.51 (0.79), residues: 40
  loop : -1.04 (0.52), residues: 146

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   0.009   0.001   PHE A 810 
 TRP   0.010   0.001   TRP A 570 
 HIS   0.009   0.001   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 2192)
  covalent geometry    : angle       0.61844 ( 2958)
  hydrogen bonds       : bond        0.03356 (   60)
  hydrogen bonds       : angle       4.76661 (  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
  68 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  584 MET cc_start: 0.2680 (tpt) cc_final: 0.2462 (tpt)
REVERT: A  590 HIS cc_start: 0.8371 (p-80) cc_final: 0.7953 (p-80)
REVERT: A  622 ILE cc_start: 0.8517 (mt) cc_final: 0.8233 (mt)
REVERT: A  784 ASN cc_start: 0.8618 (t0) cc_final: 0.8231 (t0)
REVERT: B  607 THR cc_start: 0.8824 (p) cc_final: 0.8335 (p)
REVERT: B  621 MET cc_start: 0.7109 (mtm) cc_final: 0.6810 (mpp)
REVERT: B  629 ARG cc_start: 0.6476 (mtt180) cc_final: 0.5250 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1121
  time to fit residues: 8.3180
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  : 0.082 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 = 0.4105 r_free = 0.4105 target = 0.150112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.131889 restraints weight = 6033.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.134756 restraints weight = 3743.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.136628 restraints weight = 2626.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.138017 restraints weight = 2024.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.138736 restraints weight = 1653.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.4203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2192  Z= 0.182
  Angle     :  0.685   7.296   2958  Z= 0.360
  Chirality :  0.043   0.131    352
  Planarity :  0.005   0.041    372
  Dihedral  :  6.108  20.623    300
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.51), residues: 266
  helix: -0.44 (0.59), residues: 78
  sheet: -1.61 (1.03), residues: 20
  loop : -1.17 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 606 
 TYR   0.011   0.002   TYR B 819 
 PHE   0.008   0.002   PHE A 785 
 TRP   0.015   0.002   TRP A 570 
 HIS   0.004   0.001   HIS A 804 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 2192)
  covalent geometry    : angle       0.68542 ( 2958)
  hydrogen bonds       : bond        0.03899 (   60)
  hydrogen bonds       : angle       5.13896 (  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
  57 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8300 (p-80) cc_final: 0.7915 (p-80)
REVERT: A  784 ASN cc_start: 0.8656 (t0) cc_final: 0.8312 (t0)
REVERT: B  629 ARG cc_start: 0.6491 (mtt180) cc_final: 0.5017 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1042
  time to fit residues: 6.5645
Evaluate side-chains
  42 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** B 575 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 = 0.4122 r_free = 0.4122 target = 0.151835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.133457 restraints weight = 6229.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.136233 restraints weight = 3982.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.138111 restraints weight = 2833.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.139583 restraints weight = 2193.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.140362 restraints weight = 1786.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.4514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2192  Z= 0.177
  Angle     :  0.687   5.976   2958  Z= 0.357
  Chirality :  0.045   0.164    352
  Planarity :  0.005   0.037    372
  Dihedral  :  6.089  18.690    300
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  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 are not related in a simple way.
  whole: -1.64 (0.51), residues: 266
  helix: -0.56 (0.58), residues: 80
  sheet: -1.85 (1.25), residues: 15
  loop : -1.31 (0.48), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 579 
 TYR   0.012   0.002   TYR B 819 
 PHE   0.009   0.002   PHE A 810 
 TRP   0.012   0.002   TRP A 570 
 HIS   0.004   0.001   HIS A 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 2192)
  covalent geometry    : angle       0.68689 ( 2958)
  hydrogen bonds       : bond        0.03879 (   60)
  hydrogen bonds       : angle       5.16827 (  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
  53 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8312 (p-80) cc_final: 0.7932 (p-80)
REVERT: A  622 ILE cc_start: 0.8701 (mt) cc_final: 0.8376 (mt)
REVERT: A  784 ASN cc_start: 0.8679 (t0) cc_final: 0.8332 (t0)
REVERT: B  629 ARG cc_start: 0.6479 (mtt180) cc_final: 0.4968 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0866
  time to fit residues: 5.1917
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  : 0.089 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** B 575 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 = 0.4127 r_free = 0.4127 target = 0.152162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.134040 restraints weight = 6036.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.136824 restraints weight = 3871.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.138448 restraints weight = 2763.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.139929 restraints weight = 2181.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.141065 restraints weight = 1795.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.4795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2192  Z= 0.163
  Angle     :  0.679   5.613   2958  Z= 0.352
  Chirality :  0.044   0.168    352
  Planarity :  0.005   0.037    372
  Dihedral  :  5.961  19.323    300
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  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 are not related in a simple way.
  whole: -1.53 (0.51), residues: 266
  helix: -0.40 (0.60), residues: 80
  sheet: -1.68 (1.24), residues: 15
  loop : -1.29 (0.48), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 579 
 TYR   0.011   0.002   TYR B 819 
 PHE   0.007   0.002   PHE A 810 
 TRP   0.040   0.005   TRP A 570 
 HIS   0.003   0.001   HIS A 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 2192)
  covalent geometry    : angle       0.67928 ( 2958)
  hydrogen bonds       : bond        0.03629 (   60)
  hydrogen bonds       : angle       4.89965 (  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
  56 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: A  590 HIS cc_start: 0.8312 (p-80) cc_final: 0.7904 (p-80)
REVERT: A  621 MET cc_start: 0.7547 (ptp) cc_final: 0.7343 (ptp)
REVERT: A  622 ILE cc_start: 0.8521 (mt) cc_final: 0.8129 (mt)
REVERT: A  784 ASN cc_start: 0.8672 (t0) cc_final: 0.8341 (t0)
REVERT: B  607 THR cc_start: 0.8877 (p) cc_final: 0.8467 (p)
REVERT: B  629 ARG cc_start: 0.6403 (mtt180) cc_final: 0.5008 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0862
  time to fit residues: 5.4332
Evaluate side-chains
  38 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
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:    0.1980
   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:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.4157 r_free = 0.4157 target = 0.154857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.136182 restraints weight = 6008.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.139107 restraints weight = 3795.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.140957 restraints weight = 2696.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.142404 restraints weight = 2096.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.143361 restraints weight = 1723.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.5034

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= 0.119
  Angle     :  0.650   5.766   2958  Z= 0.336
  Chirality :  0.044   0.140    352
  Planarity :  0.005   0.038    372
  Dihedral  :  5.548  17.831    300
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.37 (0.51), residues: 266
  helix: -0.27 (0.60), residues: 81
  sheet: -1.61 (1.24), residues: 15
  loop : -1.18 (0.48), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 825 
 TYR   0.010   0.001   TYR B 819 
 PHE   0.005   0.001   PHE B 810 
 TRP   0.033   0.004   TRP A 570 
 HIS   0.003   0.001   HIS A 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 2192)
  covalent geometry    : angle       0.65011 ( 2958)
  hydrogen bonds       : bond        0.03197 (   60)
  hydrogen bonds       : angle       4.65885 (  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
  55 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A  590 HIS cc_start: 0.8301 (p-80) cc_final: 0.7906 (p-80)
REVERT: A  611 MET cc_start: 0.7065 (tpp) cc_final: 0.6802 (tpp)
REVERT: A  784 ASN cc_start: 0.8656 (t0) cc_final: 0.8347 (t0)
REVERT: B  607 THR cc_start: 0.8848 (p) cc_final: 0.8511 (p)
REVERT: B  629 ARG cc_start: 0.6382 (mtt180) cc_final: 0.4995 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0858
  time to fit residues: 5.3443
Evaluate side-chains
  41 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 15 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0980
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.156088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.137345 restraints weight = 5995.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.140227 restraints weight = 3843.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.142194 restraints weight = 2764.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.143648 restraints weight = 2126.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.144743 restraints weight = 1736.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.5400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2192  Z= 0.113
  Angle     :  0.625   5.411   2958  Z= 0.324
  Chirality :  0.043   0.135    352
  Planarity :  0.004   0.037    372
  Dihedral  :  5.378  19.488    300
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  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: -1.37 (0.52), residues: 266
  helix: -0.27 (0.61), residues: 80
  sheet: -1.64 (0.89), residues: 25
  loop : -1.12 (0.50), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 825 
 TYR   0.009   0.001   TYR B 819 
 PHE   0.005   0.001   PHE A 810 
 TRP   0.031   0.004   TRP A 570 
 HIS   0.002   0.001   HIS A 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 2192)
  covalent geometry    : angle       0.62494 ( 2958)
  hydrogen bonds       : bond        0.03093 (   60)
  hydrogen bonds       : angle       4.78671 (  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
  55 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.050 
Fit side-chains
REVERT: A  590 HIS cc_start: 0.8288 (p-80) cc_final: 0.7894 (p-80)
REVERT: A  784 ASN cc_start: 0.8643 (t0) cc_final: 0.8346 (t0)
REVERT: B  607 THR cc_start: 0.8835 (p) cc_final: 0.8496 (p)
REVERT: B  629 ARG cc_start: 0.6302 (mtt180) cc_final: 0.4925 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0413
  time to fit residues: 2.6607
Evaluate side-chains
  41 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 9 optimal weight:    0.0970
   chunk 18 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 8 optimal weight:    0.1980
   chunk 23 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 0 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.4182 r_free = 0.4182 target = 0.156854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.138111 restraints weight = 5980.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.141013 restraints weight = 3824.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.142776 restraints weight = 2703.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.144296 restraints weight = 2112.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.145517 restraints weight = 1715.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.5485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   2192  Z= 0.107
  Angle     :  0.623   5.325   2958  Z= 0.322
  Chirality :  0.043   0.131    352
  Planarity :  0.004   0.037    372
  Dihedral  :  5.134  19.974    300
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  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 are not related in a simple way.
  whole: -1.54 (0.51), residues: 266
  helix: -0.28 (0.61), residues: 80
  sheet: -2.38 (0.72), residues: 35
  loop : -1.03 (0.52), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 825 
 TYR   0.009   0.001   TYR B 819 
 PHE   0.005   0.001   PHE A 785 
 TRP   0.026   0.003   TRP A 570 
 HIS   0.003   0.001   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 2192)
  covalent geometry    : angle       0.62279 ( 2958)
  hydrogen bonds       : bond        0.03061 (   60)
  hydrogen bonds       : angle       4.63751 (  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
  59 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  590 HIS cc_start: 0.8253 (p-80) cc_final: 0.7896 (p-80)
REVERT: A  784 ASN cc_start: 0.8646 (t0) cc_final: 0.8366 (t0)
REVERT: B  607 THR cc_start: 0.8874 (p) cc_final: 0.8604 (p)
REVERT: B  629 ARG cc_start: 0.6247 (mtt180) cc_final: 0.4936 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0701
  time to fit residues: 4.7500
Evaluate side-chains
  41 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0370
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.6060

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.158411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.139869 restraints weight = 6043.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.142785 restraints weight = 3826.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.144778 restraints weight = 2732.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.145982 restraints weight = 2100.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.147120 restraints weight = 1733.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.5683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2192  Z= 0.108
  Angle     :  0.610   5.116   2958  Z= 0.318
  Chirality :  0.044   0.202    352
  Planarity :  0.005   0.037    372
  Dihedral  :  5.038  20.335    300
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  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 are not related in a simple way.
  whole: -1.58 (0.51), residues: 266
  helix: -0.27 (0.61), residues: 80
  sheet: -2.53 (0.72), residues: 35
  loop : -1.05 (0.51), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 825 
 TYR   0.009   0.001   TYR B 819 
 PHE   0.004   0.001   PHE A 810 
 TRP   0.027   0.003   TRP A 570 
 HIS   0.003   0.001   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 2192)
  covalent geometry    : angle       0.61000 ( 2958)
  hydrogen bonds       : bond        0.03038 (   60)
  hydrogen bonds       : angle       4.57913 (  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  : 0.088 
Fit side-chains
REVERT: A  584 MET cc_start: 0.1919 (tpt) cc_final: 0.1658 (tpt)
REVERT: A  590 HIS cc_start: 0.8224 (p-80) cc_final: 0.7928 (p-80)
REVERT: A  784 ASN cc_start: 0.8581 (t0) cc_final: 0.8320 (t0)
REVERT: B  607 THR cc_start: 0.8848 (p) cc_final: 0.8573 (p)
REVERT: B  629 ARG cc_start: 0.6242 (mtt180) cc_final: 0.4937 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0705
  time to fit residues: 4.4988
Evaluate side-chains
  41 residues out of total 238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
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:    0.0040
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 13 optimal weight:    7.9990
   chunk 2 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0370
   chunk 1 optimal weight:    0.1980
   chunk 7 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.3470

-------------------------------------------------------------------------------
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 = 0.4216 r_free = 0.4216 target = 0.158761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.139561 restraints weight = 6022.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.142556 restraints weight = 3777.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.144630 restraints weight = 2673.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.146147 restraints weight = 2063.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.146947 restraints weight = 1672.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.5820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2192  Z= 0.102
  Angle     :  0.605   4.886   2958  Z= 0.313
  Chirality :  0.044   0.219    352
  Planarity :  0.004   0.038    372
  Dihedral  :  4.976  20.298    300
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  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 are not related in a simple way.
  whole: -1.62 (0.52), residues: 266
  helix: -0.22 (0.61), residues: 81
  sheet: -2.79 (0.70), residues: 35
  loop : -1.07 (0.52), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 825 
 TYR   0.009   0.001   TYR B 819 
 PHE   0.004   0.001   PHE A 785 
 TRP   0.021   0.002   TRP A 570 
 HIS   0.003   0.001   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 2192)
  covalent geometry    : angle       0.60540 ( 2958)
  hydrogen bonds       : bond        0.02915 (   60)
  hydrogen bonds       : angle       4.52888 (  159)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 613.05 seconds
wall clock time: 11 minutes 12.49 seconds (672.49 seconds total)