Starting phenix.real_space_refine
on Wed Sep 17 04:03:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ij2_60613/09_2025/9ij2_60613.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ij2_60613/09_2025/9ij2_60613.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ij2_60613/09_2025/9ij2_60613.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ij2_60613/09_2025/9ij2_60613.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ij2_60613/09_2025/9ij2_60613.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ij2_60613/09_2025/9ij2_60613.cif"
  }
  resolution = 3.9
  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=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      43      5.49       5
     S      25      5.16       5
     C    2229      2.51       5
     N     644      2.21       5
     O     788      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3729
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2820
          Classifications: {'peptide': 351}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 331}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 466
          Classifications: {'RNA': 22}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 3, 'rna3p': 18}
    Chain: "C"
      Number of atoms: 443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 443
          Classifications: {'RNA': 21}
          Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 11}
          Link IDs: {'rna3p': 20}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.20, per 1000 atoms: 0.32
  Number of scatterers: 3729
  At special positions: 0
  Unit cell: (66.12, 78.66, 93.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     P      43     15.00
     O     788      8.00
     N     644      7.00
     C    2229      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: 0.32
  Conformation dependent library (CDL) restraints added in 105.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  664

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 2 sheets defined
      37.3% alpha, 13.7% beta
      17 base pairs and 28 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 612 through 625
    Processing helix  chain 'A' and resid 646 through 652
    Processing helix  chain 'A' and resid 675 through 688
      removed outlier: 3.868A  pdb=" N   TYR A 679 " --> pdb=" O   ARG A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 703
    Processing helix  chain 'A' and resid 707 through 723
      removed outlier: 3.695A  pdb=" N   VAL A 711 " --> pdb=" O   ARG A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 802
      removed outlier: 4.427A  pdb=" N   SER A 785 " --> pdb=" O   GLU A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 825
      removed outlier: 3.661A  pdb=" N   ASN A 825 " --> pdb=" O   LYS A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 833
      removed outlier: 4.632A  pdb=" N   GLN A 830 " --> pdb=" O   TYR A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 837
    Processing helix  chain 'A' and resid 914 through 926
      removed outlier: 3.839A  pdb=" N   MET A 918 " --> pdb=" O   SER A 914 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 953
      removed outlier: 3.541A  pdb=" N   LYS A 943 " --> pdb=" O   PRO A 939 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ALA A 945 " --> pdb=" O   PRO A 941 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A 948 " --> pdb=" O   TYR A 944 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 967
    Processing sheet with id=AA1, first strand: chain 'A' and resid 639 through 641
      removed outlier: 3.948A  pdb=" N   GLN A 695 " --> pdb=" O   VAL A 667 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   CYS A 669 " --> pdb=" O   GLN A 695 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 769 through 774
      removed outlier: 3.856A  pdb=" N   VAL A 756 " --> pdb=" O   VAL A 774 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ASP A 743 " --> pdb=" O   GLY A 757 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   SER A 761 " --> pdb=" O   VAL A 739 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   VAL A 739 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL A 809 " --> pdb=" O   MET A 738 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   MET A 742 " --> pdb=" O   TYR A 811 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ASP A 813 " --> pdb=" O   MET A 742 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   VAL A 744 " --> pdb=" O   ASP A 813 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ARG A 812 " --> pdb=" O   PHE A 848 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   MET A 845 " --> pdb=" O   ASN A 909 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ASN A 909 " --> pdb=" O   MET A 845 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   VAL A 847 " --> pdb=" O   VAL A 907 " (cutoff:3.500A)

    104 hydrogen bonds defined for protein.
    297 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      42 hydrogen bonds
      84 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      28 stacking parallelities
  Total time for adding SS restraints: 0.78

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 894
        1.33 -     1.45: 963
        1.45 -     1.57: 1920
        1.57 -     1.69: 85
        1.69 -     1.81: 39
  Bond restraints: 3901
  Sorted by residual:
  bond pdb=" CB  TYR A 679 "
       pdb=" CG  TYR A 679 "
    ideal  model  delta    sigma   weight residual
    1.512  1.553 -0.041 2.20e-02 2.07e+03 3.50e+00
  bond pdb=" C   ILE A 828 "
       pdb=" N   PRO A 829 "
    ideal  model  delta    sigma   weight residual
    1.336  1.356 -0.020 1.20e-02 6.94e+03 2.73e+00
  bond pdb=" C   ALA A 940 "
       pdb=" N   PRO A 941 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.19e-02 7.06e+03 2.40e+00
  bond pdb=" CA  TRP A 604 "
       pdb=" CB  TRP A 604 "
    ideal  model  delta    sigma   weight residual
    1.531  1.578 -0.048 3.28e-02 9.30e+02 2.12e+00
  bond pdb=" CA  ILE A 828 "
       pdb=" C   ILE A 828 "
    ideal  model  delta    sigma   weight residual
    1.524  1.538 -0.014 1.05e-02 9.07e+03 1.74e+00
  ... (remaining 3896 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 5258
        2.52 -     5.03: 184
        5.03 -     7.55: 33
        7.55 -    10.06: 12
       10.06 -    12.58: 2
  Bond angle restraints: 5489
  Sorted by residual:
  angle pdb=" CA  TYR A 679 "
        pdb=" CB  TYR A 679 "
        pdb=" CG  TYR A 679 "
      ideal   model   delta    sigma   weight residual
     113.90  121.95   -8.05 1.80e+00 3.09e-01 2.00e+01
  angle pdb=" C   PRO A 705 "
        pdb=" N   THR A 706 "
        pdb=" CA  THR A 706 "
      ideal   model   delta    sigma   weight residual
     121.54  129.59   -8.05 1.91e+00 2.74e-01 1.78e+01
  angle pdb=" C3'   U B   1 "
        pdb=" O3'   U B   1 "
        pdb=" P     U B   2 "
      ideal   model   delta    sigma   weight residual
     120.20  125.86   -5.66 1.50e+00 4.44e-01 1.43e+01
  angle pdb=" C   ASN A 801 "
        pdb=" N   HIS A 802 "
        pdb=" CA  HIS A 802 "
      ideal   model   delta    sigma   weight residual
     121.54  128.51   -6.97 1.91e+00 2.74e-01 1.33e+01
  angle pdb=" CA  GLN A 830 "
        pdb=" CB  GLN A 830 "
        pdb=" CG  GLN A 830 "
      ideal   model   delta    sigma   weight residual
     114.10  121.39   -7.29 2.00e+00 2.50e-01 1.33e+01
  ... (remaining 5484 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.80: 2127
       29.80 -    59.60: 218
       59.60 -    89.40: 41
       89.40 -   119.19: 2
      119.19 -   148.99: 1
  Dihedral angle restraints: 2389
    sinusoidal: 1363
      harmonic: 1026
  Sorted by residual:
  dihedral pdb=" O4'   U B   2 "
           pdb=" C1'   U B   2 "
           pdb=" N1    U B   2 "
           pdb=" C2    U B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00  157.80   74.20     1      1.70e+01 3.46e-03 2.42e+01
  dihedral pdb=" CA  ILE A 654 "
           pdb=" C   ILE A 654 "
           pdb=" N   GLN A 655 "
           pdb=" CA  GLN A 655 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.66   24.34     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  GLN A 830 "
           pdb=" C   GLN A 830 "
           pdb=" N   LEU A 831 "
           pdb=" CA  LEU A 831 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.85   24.15     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 2386 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 513
       0.058 -    0.115: 111
       0.115 -    0.173: 26
       0.173 -    0.230: 5
       0.230 -    0.288: 3
  Chirality restraints: 658
  Sorted by residual:
  chirality pdb=" C3'   G C  12 "
            pdb=" C4'   G C  12 "
            pdb=" O3'   G C  12 "
            pdb=" C2'   G C  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.19   -0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CA  PHE A 950 "
            pdb=" N   PHE A 950 "
            pdb=" C   PHE A 950 "
            pdb=" CB  PHE A 950 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CA  LYS A 943 "
            pdb=" N   LYS A 943 "
            pdb=" C   LYS A 943 "
            pdb=" CB  LYS A 943 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.59e+00
  ... (remaining 655 not shown)

  Planarity restraints: 534
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 938 "    0.055 5.00e-02 4.00e+02   8.32e-02 1.11e+01
        pdb=" N   PRO A 939 "   -0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 939 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 939 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 679 "   -0.021 2.00e-02 2.50e+03   1.74e-02 6.07e+00
        pdb=" CG  TYR A 679 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 679 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 679 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 679 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 679 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 679 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 679 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 635 "    0.040 5.00e-02 4.00e+02   6.04e-02 5.83e+00
        pdb=" N   PRO A 636 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 636 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 636 "    0.033 5.00e-02 4.00e+02
  ... (remaining 531 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 873
        2.80 -     3.32: 3261
        3.32 -     3.85: 6866
        3.85 -     4.37: 7272
        4.37 -     4.90: 11285
  Nonbonded interactions: 29557
  Sorted by model distance:
  nonbonded pdb=" O   MET A 928 "
            pdb=" OH  TYR A 944 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   THR A 591 "
            pdb=" OG1 THR A 591 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   THR A 674 "
            pdb=" OG1 THR A 674 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   SER A 656 "
            pdb=" OG  SER A 656 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" O   THR A 765 "
            pdb=" OG1 THR A 765 "
     model   vdw
     2.370 3.040
  ... (remaining 29552 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.120
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4915
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      :  0.005   0.048   3901  Z= 0.232
  Angle     :  1.126  12.577   5489  Z= 0.563
  Chirality :  0.056   0.288    658
  Planarity :  0.007   0.083    534
  Dihedral  : 22.169 148.993   1725
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.80 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 32.28 %
    Favored  : 67.41 %
  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: -3.30 (0.42), residues: 347
  helix: -1.18 (0.48), residues: 98
  sheet: -0.55 (0.63), residues: 69
  loop : -3.62 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 937 
 TYR   0.042   0.003   TYR A 679 
 PHE   0.029   0.003   PHE A 950 
 TRP   0.024   0.003   TRP A 604 
 HIS   0.012   0.002   HIS A 958 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 3901)
  covalent geometry    : angle       1.12554 ( 5489)
  hydrogen bonds       : bond        0.17472 (  146)
  hydrogen bonds       : angle       7.47855 (  381)

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

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

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
REVERT: A  772 ARG cc_start: 0.5834 (mmt180) cc_final: 0.5594 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0755
  time to fit residues: 4.8364
Evaluate side-chains
  48 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0870
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0470
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.4872 r_free = 0.4872 target = 0.227943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.208193 restraints weight = 10321.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4734 r_free = 0.4734 target = 0.213087 restraints weight = 6693.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.216501 restraints weight = 4592.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.218963 restraints weight = 3282.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4804 r_free = 0.4804 target = 0.220428 restraints weight = 2413.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.4799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4896
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3901  Z= 0.119
  Angle     :  0.687   8.610   5489  Z= 0.340
  Chirality :  0.041   0.189    658
  Planarity :  0.005   0.068    534
  Dihedral  : 21.355 156.105   1027
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 29.75 %
    Favored  : 67.09 %
  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: -2.58 (0.44), residues: 347
  helix: -0.15 (0.50), residues: 99
  sheet: -0.37 (0.62), residues: 69
  loop : -3.36 (0.44), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 675 
 TYR   0.020   0.002   TYR A 679 
 PHE   0.008   0.001   PHE A 607 
 TRP   0.012   0.001   TRP A 604 
 HIS   0.002   0.000   HIS A 927 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3901)
  covalent geometry    : angle       0.68679 ( 5489)
  hydrogen bonds       : bond        0.04590 (  146)
  hydrogen bonds       : angle       5.30622 (  381)

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

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

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  641 GLU cc_start: 0.7682 (tp30) cc_final: 0.7440 (tp30)
REVERT: A  773 VAL cc_start: 0.5730 (OUTLIER) cc_final: 0.5442 (t)
  outliers start: 10
  outliers final: 4
  residues processed: 57
  average time/residue: 0.0806
  time to fit residues: 5.6150
Evaluate side-chains
  53 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  710 SER
Chi-restraints excluded: chain A residue  722 LYS
Chi-restraints excluded: chain A residue  773 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 801 ASN
A 946 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4805 r_free = 0.4805 target = 0.220011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.199514 restraints weight = 10190.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.204224 restraints weight = 6583.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.207630 restraints weight = 4522.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.210015 restraints weight = 3252.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.211746 restraints weight = 2433.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.4720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5148
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3901  Z= 0.167
  Angle     :  0.741   9.114   5489  Z= 0.365
  Chirality :  0.043   0.173    658
  Planarity :  0.005   0.065    534
  Dihedral  : 21.142 164.218   1027
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 18.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.24 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 28.16 %
    Favored  : 66.14 %
  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: -2.55 (0.45), residues: 347
  helix:  0.01 (0.50), residues: 103
  sheet: -0.38 (0.64), residues: 69
  loop : -3.48 (0.45), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 617 
 TYR   0.012   0.002   TYR A 650 
 PHE   0.021   0.002   PHE A 950 
 TRP   0.017   0.002   TRP A 604 
 HIS   0.009   0.001   HIS A 946 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3901)
  covalent geometry    : angle       0.74123 ( 5489)
  hydrogen bonds       : bond        0.05347 (  146)
  hydrogen bonds       : angle       5.25441 (  381)

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

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

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  650 TYR cc_start: 0.3273 (OUTLIER) cc_final: 0.0837 (p90)
REVERT: A  773 VAL cc_start: 0.5464 (OUTLIER) cc_final: 0.5143 (t)
REVERT: A  928 MET cc_start: 0.7372 (ppp) cc_final: 0.6178 (ppp)
  outliers start: 18
  outliers final: 8
  residues processed: 69
  average time/residue: 0.0951
  time to fit residues: 7.6949
Evaluate side-chains
  64 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 TRP
Chi-restraints excluded: chain A residue  604 TRP
Chi-restraints excluded: chain A residue  650 TYR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  735 LYS
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  777 MET
Chi-restraints excluded: chain A residue  910 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 18 optimal weight:    0.4980
   chunk 31 optimal weight:    0.4980
   chunk 24 optimal weight:   10.0000
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 946 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.223568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.204009 restraints weight = 9829.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4695 r_free = 0.4695 target = 0.208674 restraints weight = 6389.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4725 r_free = 0.4725 target = 0.211970 restraints weight = 4404.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.214352 restraints weight = 3177.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4764 r_free = 0.4764 target = 0.215947 restraints weight = 2370.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.4761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5007
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3901  Z= 0.122
  Angle     :  0.671   8.138   5489  Z= 0.328
  Chirality :  0.040   0.182    658
  Planarity :  0.005   0.063    534
  Dihedral  : 21.040 163.926   1027
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 28.16 %
    Favored  : 65.51 %
  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: -2.33 (0.45), residues: 347
  helix:  0.19 (0.50), residues: 103
  sheet: -0.37 (0.62), residues: 70
  loop : -3.32 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 617 
 TYR   0.026   0.002   TYR A 679 
 PHE   0.011   0.002   PHE A 950 
 TRP   0.015   0.002   TRP A 769 
 HIS   0.005   0.001   HIS A 946 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 3901)
  covalent geometry    : angle       0.67074 ( 5489)
  hydrogen bonds       : bond        0.04214 (  146)
  hydrogen bonds       : angle       5.01064 (  381)

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

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

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.5594 (tpt) cc_final: 0.5178 (tpt)
REVERT: A  641 GLU cc_start: 0.7751 (tp30) cc_final: 0.7492 (tp30)
REVERT: A  650 TYR cc_start: 0.3655 (OUTLIER) cc_final: 0.1760 (p90)
REVERT: A  773 VAL cc_start: 0.5665 (OUTLIER) cc_final: 0.5316 (t)
REVERT: A  928 MET cc_start: 0.7947 (ppp) cc_final: 0.7353 (tmm)
  outliers start: 20
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0865
  time to fit residues: 7.2018
Evaluate side-chains
  60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 PHE
Chi-restraints excluded: chain A residue  586 TRP
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  650 TYR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  722 LYS
Chi-restraints excluded: chain A residue  735 LYS
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  844 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 30 optimal weight:    0.3980
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 832 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4800 r_free = 0.4800 target = 0.219005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.198733 restraints weight = 10696.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.203172 restraints weight = 7036.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.206467 restraints weight = 4919.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.208923 restraints weight = 3604.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.210500 restraints weight = 2720.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.4708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5192
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3901  Z= 0.162
  Angle     :  0.714  11.007   5489  Z= 0.350
  Chirality :  0.042   0.160    658
  Planarity :  0.005   0.064    534
  Dihedral  : 21.001 169.844   1027
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 19.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  7.28 %
    Allowed  : 27.85 %
    Favored  : 64.87 %
  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: -2.41 (0.45), residues: 347
  helix:  0.14 (0.51), residues: 103
  sheet: -0.39 (0.61), residues: 70
  loop : -3.39 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 709 
 TYR   0.027   0.002   TYR A 679 
 PHE   0.014   0.002   PHE A 607 
 TRP   0.015   0.002   TRP A 769 
 HIS   0.005   0.001   HIS A 946 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3901)
  covalent geometry    : angle       0.71406 ( 5489)
  hydrogen bonds       : bond        0.05090 (  146)
  hydrogen bonds       : angle       5.08310 (  381)

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

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

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 52
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.5850 (tpt) cc_final: 0.5470 (tpt)
REVERT: A  650 TYR cc_start: 0.3087 (OUTLIER) cc_final: 0.1028 (p90)
REVERT: A  719 MET cc_start: 0.5422 (mmt) cc_final: 0.5090 (mmm)
REVERT: A  773 VAL cc_start: 0.5657 (OUTLIER) cc_final: 0.5340 (t)
REVERT: A  842 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.7683 (p90)
  outliers start: 23
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0804
  time to fit residues: 6.9029
Evaluate side-chains
  61 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  586 TRP
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  650 TYR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  735 LYS
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  842 HIS
Chi-restraints excluded: chain A residue  844 LYS
Chi-restraints excluded: chain A residue  910 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 37 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.213979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.194218 restraints weight = 10996.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.198679 restraints weight = 7172.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.201825 restraints weight = 4984.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.204101 restraints weight = 3633.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.205772 restraints weight = 2737.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.4656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5315
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3901  Z= 0.193
  Angle     :  0.802  11.410   5489  Z= 0.392
  Chirality :  0.045   0.171    658
  Planarity :  0.005   0.062    534
  Dihedral  : 20.988 173.750   1027
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 24.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.24 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 30.70 %
    Favored  : 62.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.69 (0.45), residues: 347
  helix: -0.25 (0.50), residues: 109
  sheet: -0.51 (0.61), residues: 70
  loop : -3.58 (0.47), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 709 
 TYR   0.021   0.002   TYR A 679 
 PHE   0.020   0.002   PHE A 607 
 TRP   0.016   0.002   TRP A 769 
 HIS   0.004   0.001   HIS A 957 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 3901)
  covalent geometry    : angle       0.80180 ( 5489)
  hydrogen bonds       : bond        0.05848 (  146)
  hydrogen bonds       : angle       5.39022 (  381)

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

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

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.5692 (tpt) cc_final: 0.5403 (tpt)
REVERT: A  650 TYR cc_start: 0.2990 (OUTLIER) cc_final: 0.1066 (p90)
REVERT: A  652 ARG cc_start: 0.4885 (OUTLIER) cc_final: 0.4519 (tpm-80)
REVERT: A  719 MET cc_start: 0.6287 (mmt) cc_final: 0.6043 (mmm)
REVERT: A  735 LYS cc_start: 0.4483 (OUTLIER) cc_final: 0.4211 (pttm)
REVERT: A  769 TRP cc_start: 0.6696 (m100) cc_final: 0.6293 (m-10)
REVERT: A  773 VAL cc_start: 0.5429 (OUTLIER) cc_final: 0.5089 (t)
REVERT: A  842 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.7615 (p90)
  outliers start: 20
  outliers final: 11
  residues processed: 68
  average time/residue: 0.0692
  time to fit residues: 5.7780
Evaluate side-chains
  65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 TRP
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  650 TYR
Chi-restraints excluded: chain A residue  652 ARG
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  735 LYS
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  777 MET
Chi-restraints excluded: chain A residue  784 ASP
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  842 HIS
Chi-restraints excluded: chain A residue  844 LYS
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  962 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 38 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0470
   chunk 24 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 31 optimal weight:    0.4980
   chunk 5 optimal weight:    5.9990
   overall best weight:    0.8480

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

Flipped N/Q/H residues before XYZ refinement:
** A 695 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 = 0.4830 r_free = 0.4830 target = 0.221428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.203574 restraints weight = 11741.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.207295 restraints weight = 7639.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4725 r_free = 0.4725 target = 0.210429 restraints weight = 5409.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.212437 restraints weight = 3988.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.213974 restraints weight = 3067.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.4754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5154
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3901  Z= 0.130
  Angle     :  0.699  10.498   5489  Z= 0.337
  Chirality :  0.041   0.162    658
  Planarity :  0.005   0.062    534
  Dihedral  : 20.646 163.871   1027
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 19.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.80 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 33.23 %
    Favored  : 62.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.42 (0.46), residues: 347
  helix:  0.14 (0.51), residues: 109
  sheet: -0.45 (0.61), residues: 70
  loop : -3.49 (0.47), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 709 
 TYR   0.010   0.002   TYR A 608 
 PHE   0.019   0.002   PHE A 969 
 TRP   0.008   0.001   TRP A 769 
 HIS   0.003   0.001   HIS A 958 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3901)
  covalent geometry    : angle       0.69868 ( 5489)
  hydrogen bonds       : bond        0.04725 (  146)
  hydrogen bonds       : angle       5.02755 (  381)

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

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

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.5841 (tpt) cc_final: 0.5570 (tpt)
REVERT: A  650 TYR cc_start: 0.3143 (OUTLIER) cc_final: 0.1763 (p90)
REVERT: A  773 VAL cc_start: 0.5458 (OUTLIER) cc_final: 0.5059 (t)
REVERT: A  844 LYS cc_start: 0.3156 (OUTLIER) cc_final: 0.2897 (ptpt)
  outliers start: 15
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0861
  time to fit residues: 6.7635
Evaluate side-chains
  64 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 TRP
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  650 TYR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  735 LYS
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  784 ASP
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  844 LYS
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  962 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 19 optimal weight:    0.2980
   chunk 30 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9990
   chunk 38 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 695 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 = 0.4788 r_free = 0.4788 target = 0.217006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.199994 restraints weight = 11582.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.203704 restraints weight = 7679.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.206216 restraints weight = 5396.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.208020 restraints weight = 4012.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.209448 restraints weight = 3122.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.4712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5273
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3901  Z= 0.179
  Angle     :  0.776  10.084   5489  Z= 0.379
  Chirality :  0.043   0.188    658
  Planarity :  0.005   0.061    534
  Dihedral  : 20.681 159.117   1027
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 24.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.39 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 33.54 %
    Favored  : 60.76 %
  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: -2.60 (0.45), residues: 347
  helix:  0.05 (0.51), residues: 106
  sheet: -0.60 (0.60), residues: 70
  loop : -3.56 (0.47), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 709 
 TYR   0.011   0.002   TYR A 608 
 PHE   0.018   0.002   PHE A 969 
 TRP   0.015   0.002   TRP A 769 
 HIS   0.004   0.001   HIS A 958 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 3901)
  covalent geometry    : angle       0.77568 ( 5489)
  hydrogen bonds       : bond        0.05612 (  146)
  hydrogen bonds       : angle       5.26256 (  381)

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

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

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.5684 (tpt) cc_final: 0.5460 (tpt)
REVERT: A  613 MET cc_start: 0.5824 (mtt) cc_final: 0.5281 (mtt)
REVERT: A  650 TYR cc_start: 0.3477 (OUTLIER) cc_final: 0.1609 (p90)
REVERT: A  769 TRP cc_start: 0.6746 (m100) cc_final: 0.6250 (m-10)
REVERT: A  773 VAL cc_start: 0.5318 (OUTLIER) cc_final: 0.4966 (t)
  outliers start: 18
  outliers final: 12
  residues processed: 68
  average time/residue: 0.0742
  time to fit residues: 6.2432
Evaluate side-chains
  64 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 TRP
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  650 TYR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  784 ASP
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  844 LYS
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  969 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 11 optimal weight:    0.6980
   chunk 1 optimal weight:    7.9990
   chunk 9 optimal weight:    0.0470
   chunk 7 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6880

-------------------------------------------------------------------------------
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 = 0.4837 r_free = 0.4837 target = 0.222353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.204085 restraints weight = 11388.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.208255 restraints weight = 7535.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4730 r_free = 0.4730 target = 0.211169 restraints weight = 5295.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.213327 restraints weight = 3921.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.214925 restraints weight = 2976.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.4761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5079
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3901  Z= 0.131
  Angle     :  0.742  14.670   5489  Z= 0.354
  Chirality :  0.041   0.179    658
  Planarity :  0.005   0.062    534
  Dihedral  : 20.486 156.203   1027
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 17.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 33.86 %
    Favored  : 61.39 %
  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: -2.21 (0.46), residues: 347
  helix:  0.44 (0.53), residues: 102
  sheet: -0.51 (0.60), residues: 70
  loop : -3.22 (0.47), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 709 
 TYR   0.017   0.002   TYR A 608 
 PHE   0.017   0.002   PHE A 969 
 TRP   0.013   0.002   TRP A 728 
 HIS   0.002   0.001   HIS A 958 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3901)
  covalent geometry    : angle       0.74197 ( 5489)
  hydrogen bonds       : bond        0.04513 (  146)
  hydrogen bonds       : angle       4.92952 (  381)

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

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

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A  650 TYR cc_start: 0.3398 (OUTLIER) cc_final: 0.1992 (p90)
REVERT: A  769 TRP cc_start: 0.6226 (m100) cc_final: 0.5758 (m100)
REVERT: A  773 VAL cc_start: 0.5291 (OUTLIER) cc_final: 0.4861 (t)
  outliers start: 15
  outliers final: 9
  residues processed: 62
  average time/residue: 0.0799
  time to fit residues: 5.9580
Evaluate side-chains
  59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 TRP
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  650 TYR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  735 LYS
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  910 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0980
   chunk 24 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
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 = 0.4769 r_free = 0.4769 target = 0.215501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.198994 restraints weight = 11987.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.202667 restraints weight = 7993.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4674 r_free = 0.4674 target = 0.205208 restraints weight = 5656.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.207038 restraints weight = 4206.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.208486 restraints weight = 3253.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.4701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5280
moved from start:          0.4633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3901  Z= 0.205
  Angle     :  0.858  14.654   5489  Z= 0.415
  Chirality :  0.045   0.193    658
  Planarity :  0.005   0.059    534
  Dihedral  : 20.640 160.724   1027
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 25.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.39 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 34.49 %
    Favored  : 61.39 %
  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: -2.70 (0.45), residues: 347
  helix: -0.19 (0.50), residues: 107
  sheet: -0.83 (0.59), residues: 70
  loop : -3.43 (0.47), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 709 
 TYR   0.015   0.003   TYR A 679 
 PHE   0.019   0.003   PHE A 607 
 TRP   0.014   0.002   TRP A 604 
 HIS   0.008   0.001   HIS A 927 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 3901)
  covalent geometry    : angle       0.85810 ( 5489)
  hydrogen bonds       : bond        0.05997 (  146)
  hydrogen bonds       : angle       5.48508 (  381)

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

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

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  694 Ramachandran restraints generated.
    347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: A  598 THR cc_start: 0.6826 (p) cc_final: 0.6616 (p)
REVERT: A  613 MET cc_start: 0.5894 (mtt) cc_final: 0.5332 (mtt)
REVERT: A  650 TYR cc_start: 0.3395 (OUTLIER) cc_final: 0.1703 (p90)
REVERT: A  719 MET cc_start: 0.6047 (mmm) cc_final: 0.5696 (mmm)
REVERT: A  773 VAL cc_start: 0.5311 (OUTLIER) cc_final: 0.5087 (t)
  outliers start: 13
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0813
  time to fit residues: 6.2192
Evaluate side-chains
  62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 TRP
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  650 TYR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  969 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4823 r_free = 0.4823 target = 0.221052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.205203 restraints weight = 11786.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.208663 restraints weight = 7896.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.211321 restraints weight = 5613.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4747 r_free = 0.4747 target = 0.213028 restraints weight = 4142.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4761 r_free = 0.4761 target = 0.214424 restraints weight = 3192.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.4762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5075
moved from start:          0.4688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3901  Z= 0.141
  Angle     :  0.774  16.407   5489  Z= 0.371
  Chirality :  0.042   0.180    658
  Planarity :  0.005   0.061    534
  Dihedral  : 20.468 156.368   1027
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 20.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 35.44 %
    Favored  : 61.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.50 (0.46), residues: 347
  helix:  0.00 (0.50), residues: 107
  sheet: -0.71 (0.59), residues: 70
  loop : -3.33 (0.49), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 709 
 TYR   0.022   0.002   TYR A 944 
 PHE   0.011   0.002   PHE A 607 
 TRP   0.012   0.001   TRP A 769 
 HIS   0.004   0.001   HIS A 927 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3901)
  covalent geometry    : angle       0.77428 ( 5489)
  hydrogen bonds       : bond        0.04641 (  146)
  hydrogen bonds       : angle       5.19213 (  381)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 824.71 seconds
wall clock time: 15 minutes 6.74 seconds (906.74 seconds total)