Starting phenix.real_space_refine
on Fri Aug 22 12:55:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8edl_28035/08_2025/8edl_28035.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8edl_28035/08_2025/8edl_28035.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8edl_28035/08_2025/8edl_28035.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8edl_28035/08_2025/8edl_28035.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8edl_28035/08_2025/8edl_28035.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8edl_28035/08_2025/8edl_28035.cif"
  }
  resolution = 3.7
  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=   0.002
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      15      5.16       5
     C    1552      2.51       5
     N     469      2.21       5
     O     434      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2470
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 2470
          Classifications: {'peptide': 395}
          Incomplete info: {'truncation_to_alanine': 224}
          Link IDs: {'PTRANS': 11, 'TRANS': 383}
          Chain breaks: 5
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 674
          Unresolved non-hydrogen angles: 856
          Unresolved non-hydrogen dihedrals: 514
          Unresolved non-hydrogen chiralities: 84
          Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 15, 'ASP:plan': 19, 'ARG:plan': 7, 'PHE:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 16, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 317
  Time building chain proxies: 0.74, per 1000 atoms: 0.30
  Number of scatterers: 2470
  At special positions: 0
  Unit cell: (94.64, 79.04, 66.56, 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      15     16.00
     O     434      8.00
     N     469      7.00
     C    1552      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: 0.15
  Conformation dependent library (CDL) restraints added in 110.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  758

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 0 sheets defined
      78.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 582 through 588
    Processing helix  chain 'A' and resid 592 through 618
    Processing helix  chain 'A' and resid 678 through 697
      removed outlier: 3.884A  pdb=" N   TRP A 696 " --> pdb=" O   TYR A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 721
      removed outlier: 4.479A  pdb=" N   LEU A 704 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 731
    Processing helix  chain 'A' and resid 734 through 747
      removed outlier: 3.572A  pdb=" N   ALA A 742 " --> pdb=" O   PHE A 738 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER A 743 " --> pdb=" O   MET A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 766
    Processing helix  chain 'A' and resid 770 through 794
      removed outlier: 3.538A  pdb=" N   LEU A 790 " --> pdb=" O   GLN A 786 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ILE A 791 " --> pdb=" O   ALA A 787 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU A 792 " --> pdb=" O   THR A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 857
      removed outlier: 4.611A  pdb=" N   GLY A 849 " --> pdb=" O   CYS A 845 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL A 850 " --> pdb=" O   ALA A 846 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   CYS A 851 " --> pdb=" O   LEU A 847 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASN A 857 " --> pdb=" O   GLN A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 902
      removed outlier: 3.788A  pdb=" N   MET A 895 " --> pdb=" O   VAL A 891 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   MET A 902 " --> pdb=" O   LEU A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 924
    Processing helix  chain 'A' and resid 926 through 928
      No H-bonds generated for 'chain 'A' and resid 926 through 928'
    Processing helix  chain 'A' and resid 929 through 943
      removed outlier: 3.515A  pdb=" N   LYS A 943 " --> pdb=" O   ASN A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 974
    Processing helix  chain 'A' and resid 979 through 984
    Processing helix  chain 'A' and resid 988 through 1001
      removed outlier: 4.023A  pdb=" N   VAL A1001 " --> pdb=" O   ARG A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1024
    Processing helix  chain 'A' and resid 1033 through 1047
      removed outlier: 3.663A  pdb=" N   PHE A1037 " --> pdb=" O   GLN A1033 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ASP A1047 " --> pdb=" O   GLU A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1081
      removed outlier: 3.610A  pdb=" N   ALA A1081 " --> pdb=" O   VAL A1077 " (cutoff:3.500A)

    219 hydrogen bonds defined for protein.
    651 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: 0.25

  Time building geometry restraints manager: 0.20 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: 864
        1.34 -     1.46: 462
        1.46 -     1.58: 1154
        1.58 -     1.70: 0
        1.70 -     1.81: 24
  Bond restraints: 2504
  Sorted by residual:
  bond pdb=" N   GLN A 963 "
       pdb=" CA  GLN A 963 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.024 1.21e-02 6.83e+03 3.79e+00
  bond pdb=" C   GLU A 962 "
       pdb=" N   GLN A 963 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 1.31e-02 5.83e+03 2.56e+00
  bond pdb=" CG  MET A1041 "
       pdb=" SD  MET A1041 "
    ideal  model  delta    sigma   weight residual
    1.803  1.776  0.027 2.50e-02 1.60e+03 1.15e+00
  bond pdb=" CA  GLY A 751 "
       pdb=" C   GLY A 751 "
    ideal  model  delta    sigma   weight residual
    1.518  1.508  0.010 1.02e-02 9.61e+03 1.01e+00
  bond pdb=" C   GLY A 751 "
       pdb=" O   GLY A 751 "
    ideal  model  delta    sigma   weight residual
    1.230  1.236 -0.006 9.40e-03 1.13e+04 4.76e-01
  ... (remaining 2499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 3322
        1.27 -     2.54: 84
        2.54 -     3.80: 11
        3.80 -     5.07: 4
        5.07 -     6.34: 3
  Bond angle restraints: 3424
  Sorted by residual:
  angle pdb=" CG  MET A1041 "
        pdb=" SD  MET A1041 "
        pdb=" CE  MET A1041 "
      ideal   model   delta    sigma   weight residual
     100.90   94.56    6.34 2.20e+00 2.07e-01 8.31e+00
  angle pdb=" C   LYS A 908 "
        pdb=" N   VAL A 909 "
        pdb=" CA  VAL A 909 "
      ideal   model   delta    sigma   weight residual
     121.97  126.66   -4.69 1.80e+00 3.09e-01 6.79e+00
  angle pdb=" CA  MET A 992 "
        pdb=" CB  MET A 992 "
        pdb=" CG  MET A 992 "
      ideal   model   delta    sigma   weight residual
     114.10  118.89   -4.79 2.00e+00 2.50e-01 5.74e+00
  angle pdb=" CA  VAL A 903 "
        pdb=" CB  VAL A 903 "
        pdb=" CG1 VAL A 903 "
      ideal   model   delta    sigma   weight residual
     110.40  114.25   -3.85 1.70e+00 3.46e-01 5.12e+00
  angle pdb=" C   LYS A1040 "
        pdb=" N   MET A1041 "
        pdb=" CA  MET A1041 "
      ideal   model   delta    sigma   weight residual
     120.31  117.07    3.24 1.52e+00 4.33e-01 4.54e+00
  ... (remaining 3419 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.97: 1322
       10.97 -    21.94: 93
       21.94 -    32.91: 34
       32.91 -    43.88: 17
       43.88 -    54.85: 2
  Dihedral angle restraints: 1468
    sinusoidal: 316
      harmonic: 1152
  Sorted by residual:
  dihedral pdb=" CA  LEU A1079 "
           pdb=" C   LEU A1079 "
           pdb=" N   LEU A1080 "
           pdb=" CA  LEU A1080 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.38  -14.62     0      5.00e+00 4.00e-02 8.55e+00
  dihedral pdb=" CA  PHE A 894 "
           pdb=" CB  PHE A 894 "
           pdb=" CG  PHE A 894 "
           pdb=" CD1 PHE A 894 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -20.00   34.85  -54.85     2      2.00e+01 2.50e-03 8.02e+00
  dihedral pdb=" CA  LEU A 933 "
           pdb=" CB  LEU A 933 "
           pdb=" CG  LEU A 933 "
           pdb=" CD1 LEU A 933 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.02   43.98     3      1.50e+01 4.44e-03 7.91e+00
  ... (remaining 1465 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 268
       0.027 -    0.054: 100
       0.054 -    0.081: 38
       0.081 -    0.108: 10
       0.108 -    0.135: 1
  Chirality restraints: 417
  Sorted by residual:
  chirality pdb=" CA  MET A1041 "
            pdb=" N   MET A1041 "
            pdb=" C   MET A1041 "
            pdb=" CB  MET A1041 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  PRO A 733 "
            pdb=" N   PRO A 733 "
            pdb=" C   PRO A 733 "
            pdb=" CB  PRO A 733 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.79e-01
  chirality pdb=" CA  ILE A 766 "
            pdb=" N   ILE A 766 "
            pdb=" C   ILE A 766 "
            pdb=" CB  ILE A 766 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.51e-01
  ... (remaining 414 not shown)

  Planarity restraints: 452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 962 "   -0.017 2.00e-02 2.50e+03   3.37e-02 1.14e+01
        pdb=" C   GLU A 962 "    0.058 2.00e-02 2.50e+03
        pdb=" O   GLU A 962 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLN A 963 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1037 "   -0.014 2.00e-02 2.50e+03   1.27e-02 2.83e+00
        pdb=" CG  PHE A1037 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1037 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1037 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1037 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1037 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1037 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 889 "    0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO A 890 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 890 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 890 "    0.020 5.00e-02 4.00e+02
  ... (remaining 449 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 782
        2.83 -     3.34: 2562
        3.34 -     3.86: 3964
        3.86 -     4.38: 4031
        4.38 -     4.90: 6826
  Nonbonded interactions: 18165
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 952 "
            pdb=" ND2 ASN A 957 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" O   LYS A 584 "
            pdb=" OG  SER A 587 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   TRP A 784 "
            pdb=" OG1 THR A 788 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   PHE A 944 "
            pdb=" N   LEU A 952 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" O   LEU A 792 "
            pdb=" NE2 HIS A 906 "
     model   vdw
     2.476 3.120
  ... (remaining 18160 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.680
  Find NCS groups from input model:        0.010
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6243
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      :  0.002   0.027   2504  Z= 0.126
  Angle     :  0.520   6.341   3424  Z= 0.313
  Chirality :  0.033   0.135    417
  Planarity :  0.003   0.035    452
  Dihedral  : 11.073  54.855    710
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.09 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.83 (0.45), residues: 383
  helix:  2.73 (0.30), residues: 275
  sheet:  None (None), residues: 0
  loop : -0.45 (0.69), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 765 
 TYR   0.005   0.001   TYR A1044 
 PHE   0.029   0.002   PHE A1037 
 TRP   0.009   0.002   TRP A 696 
 HIS   0.001   0.001   HIS A 906 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 2504)
  covalent geometry    : angle       0.51984 ( 3424)
  hydrogen bonds       : bond        0.17878 (  219)
  hydrogen bonds       : angle       4.89347 (  651)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1037 PHE cc_start: 0.7781 (t80) cc_final: 0.7533 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0508
  time to fit residues: 4.0835
Evaluate side-chains
  43 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0470
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A 684 GLN
A 712 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.109357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.090357 restraints weight = 9730.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.092004 restraints weight = 6888.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.093061 restraints weight = 5431.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.093700 restraints weight = 4638.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.094235 restraints weight = 4193.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2504  Z= 0.113
  Angle     :  0.486   7.361   3424  Z= 0.257
  Chirality :  0.034   0.118    417
  Planarity :  0.004   0.032    452
  Dihedral  :  3.217  14.239    406
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.61 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 13.08 %
    Favored  : 83.08 %
  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:  3.21 (0.44), residues: 383
  helix:  2.81 (0.29), residues: 294
  sheet:  None (None), residues: 0
  loop : -0.33 (0.72), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1038 
 TYR   0.009   0.002   TYR A 998 
 PHE   0.007   0.001   PHE A 945 
 TRP   0.014   0.002   TRP A 837 
 HIS   0.006   0.001   HIS A 781 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 2504)
  covalent geometry    : angle       0.48590 ( 3424)
  hydrogen bonds       : bond        0.03694 (  219)
  hydrogen bonds       : angle       3.39399 (  651)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.057 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.7194 (OUTLIER) cc_final: 0.6928 (p)
REVERT: A  985 GLN cc_start: 0.4975 (mp10) cc_final: 0.4137 (mm-40)
REVERT: A 1085 LEU cc_start: 0.7717 (mt) cc_final: 0.7438 (mp)
  outliers start: 5
  outliers final: 1
  residues processed: 54
  average time/residue: 0.0570
  time to fit residues: 3.5788
Evaluate side-chains
  44 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  587 SER
Chi-restraints excluded: chain A residue  904 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 781 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.102291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.082203 restraints weight = 10122.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.083663 restraints weight = 7185.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.084657 restraints weight = 5800.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.084914 restraints weight = 5044.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.085455 restraints weight = 4732.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.6898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2504  Z= 0.163
  Angle     :  0.547   7.711   3424  Z= 0.293
  Chirality :  0.035   0.111    417
  Planarity :  0.004   0.033    452
  Dihedral  :  3.573  17.364    406
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.61 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.46 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.76 (0.43), residues: 383
  helix:  2.49 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.69 (0.70), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 997 
 TYR   0.016   0.003   TYR A 998 
 PHE   0.016   0.003   PHE A1037 
 TRP   0.017   0.002   TRP A 777 
 HIS   0.003   0.001   HIS A 982 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 2504)
  covalent geometry    : angle       0.54715 ( 3424)
  hydrogen bonds       : bond        0.04233 (  219)
  hydrogen bonds       : angle       3.71072 (  651)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.7584 (t) cc_final: 0.7275 (p)
REVERT: A  777 TRP cc_start: 0.7355 (t60) cc_final: 0.7110 (t60)
REVERT: A 1085 LEU cc_start: 0.8062 (mt) cc_final: 0.7792 (mp)
  outliers start: 4
  outliers final: 2
  residues processed: 45
  average time/residue: 0.0315
  time to fit residues: 1.8395
Evaluate side-chains
  43 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  696 TRP
Chi-restraints excluded: chain A residue  904 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0870
   chunk 17 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.7762

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

Flipped N/Q/H residues before XYZ refinement:
** A 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 786 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.100130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.079649 restraints weight = 9957.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.081107 restraints weight = 7101.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.082016 restraints weight = 5741.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.082341 restraints weight = 5033.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.082747 restraints weight = 4720.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.8440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2504  Z= 0.170
  Angle     :  0.554  10.377   3424  Z= 0.299
  Chirality :  0.036   0.123    417
  Planarity :  0.003   0.034    452
  Dihedral  :  3.771  15.351    406
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.69 %
    Favored  : 79.23 %
  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:  2.47 (0.42), residues: 383
  helix:  2.30 (0.29), residues: 297
  sheet:  None (None), residues: 0
  loop : -0.83 (0.68), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1000 
 TYR   0.011   0.002   TYR A 998 
 PHE   0.010   0.002   PHE A 843 
 TRP   0.006   0.002   TRP A 777 
 HIS   0.006   0.001   HIS A 982 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 2504)
  covalent geometry    : angle       0.55364 ( 3424)
  hydrogen bonds       : bond        0.04214 (  219)
  hydrogen bonds       : angle       3.80607 (  651)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.066 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.8045 (t) cc_final: 0.7789 (p)
REVERT: A  686 LYS cc_start: 0.8244 (tppt) cc_final: 0.7752 (mmmt)
REVERT: A 1085 LEU cc_start: 0.8230 (mt) cc_final: 0.7937 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 44
  average time/residue: 0.0409
  time to fit residues: 2.2816
Evaluate side-chains
  43 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue  696 TRP
Chi-restraints excluded: chain A residue  904 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 18 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.3988 r_free = 0.3988 target = 0.099897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.079024 restraints weight = 9958.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.080445 restraints weight = 7130.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.081344 restraints weight = 5805.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.081781 restraints weight = 5118.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.082226 restraints weight = 4757.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.8963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2504  Z= 0.134
  Angle     :  0.486   6.044   3424  Z= 0.265
  Chirality :  0.035   0.110    417
  Planarity :  0.003   0.031    452
  Dihedral  :  3.423  14.547    406
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 20.00 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.91 (0.43), residues: 383
  helix:  2.58 (0.29), residues: 297
  sheet:  None (None), residues: 0
  loop : -0.52 (0.71), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A1000 
 TYR   0.008   0.001   TYR A 998 
 PHE   0.013   0.002   PHE A 843 
 TRP   0.011   0.002   TRP A1048 
 HIS   0.003   0.001   HIS A 906 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 2504)
  covalent geometry    : angle       0.48638 ( 3424)
  hydrogen bonds       : bond        0.03743 (  219)
  hydrogen bonds       : angle       3.54948 (  651)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A  587 SER cc_start: 0.7903 (t) cc_final: 0.7650 (p)
REVERT: A  686 LYS cc_start: 0.8258 (tppt) cc_final: 0.7831 (mmmm)
REVERT: A 1085 LEU cc_start: 0.8263 (mt) cc_final: 0.7949 (mp)
  outliers start: 2
  outliers final: 2
  residues processed: 44
  average time/residue: 0.0455
  time to fit residues: 2.5294
Evaluate side-chains
  41 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue  904 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 11 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 17 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3993 r_free = 0.3993 target = 0.100145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.079742 restraints weight = 9890.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.081144 restraints weight = 7094.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.081899 restraints weight = 5765.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.082652 restraints weight = 5112.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.082955 restraints weight = 4691.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.9231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2504  Z= 0.111
  Angle     :  0.482   6.339   3424  Z= 0.257
  Chirality :  0.034   0.123    417
  Planarity :  0.003   0.027    452
  Dihedral  :  3.243  13.252    406
  Min Nonbonded Distance : 2.670

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 21.54 %
    Favored  : 76.15 %
  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:  3.15 (0.44), residues: 383
  helix:  2.71 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.28 (0.74), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1000 
 TYR   0.006   0.001   TYR A1044 
 PHE   0.013   0.001   PHE A 843 
 TRP   0.006   0.001   TRP A 696 
 HIS   0.002   0.000   HIS A 982 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 2504)
  covalent geometry    : angle       0.48196 ( 3424)
  hydrogen bonds       : bond        0.03505 (  219)
  hydrogen bonds       : angle       3.41104 (  651)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.7971 (t) cc_final: 0.7697 (p)
REVERT: A  686 LYS cc_start: 0.8248 (tppt) cc_final: 0.7852 (mmmm)
REVERT: A  738 PHE cc_start: 0.7821 (m-80) cc_final: 0.7592 (m-80)
REVERT: A 1085 LEU cc_start: 0.8217 (mt) cc_final: 0.7911 (mp)
  outliers start: 3
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0548
  time to fit residues: 3.1011
Evaluate side-chains
  46 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  904 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0060
   chunk 0 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0570
   overall best weight:    0.8118

-------------------------------------------------------------------------------
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 = 0.4004 r_free = 0.4004 target = 0.100626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.080457 restraints weight = 9873.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.081959 restraints weight = 7044.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.082781 restraints weight = 5689.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.083523 restraints weight = 5013.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.083825 restraints weight = 4590.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.9461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2504  Z= 0.109
  Angle     :  0.498   6.760   3424  Z= 0.264
  Chirality :  0.034   0.108    417
  Planarity :  0.003   0.041    452
  Dihedral  :  3.224  13.125    406
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 23.08 %
    Favored  : 75.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.34 (0.44), residues: 383
  helix:  2.82 (0.30), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.13 (0.75), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1000 
 TYR   0.006   0.001   TYR A 998 
 PHE   0.029   0.002   PHE A1037 
 TRP   0.012   0.001   TRP A1048 
 HIS   0.001   0.000   HIS A 982 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 2504)
  covalent geometry    : angle       0.49822 ( 3424)
  hydrogen bonds       : bond        0.03371 (  219)
  hydrogen bonds       : angle       3.30469 (  651)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.8025 (t) cc_final: 0.7689 (p)
REVERT: A  686 LYS cc_start: 0.8155 (tppt) cc_final: 0.7763 (mmmm)
REVERT: A  992 MET cc_start: 0.7664 (mmm) cc_final: 0.7393 (mmm)
REVERT: A 1085 LEU cc_start: 0.8210 (mt) cc_final: 0.7903 (mp)
  outliers start: 2
  outliers final: 1
  residues processed: 44
  average time/residue: 0.0479
  time to fit residues: 2.6782
Evaluate side-chains
  41 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  991 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0370
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    0.9862

-------------------------------------------------------------------------------
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 = 0.3992 r_free = 0.3992 target = 0.099975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.080068 restraints weight = 10095.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.081276 restraints weight = 7152.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.082405 restraints weight = 5847.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.082866 restraints weight = 5109.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.083427 restraints weight = 4717.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.9705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2504  Z= 0.110
  Angle     :  0.485   6.017   3424  Z= 0.252
  Chirality :  0.034   0.108    417
  Planarity :  0.003   0.028    452
  Dihedral  :  3.183  13.369    406
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 22.31 %
    Favored  : 75.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.32 (0.44), residues: 383
  helix:  2.80 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.16 (0.77), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1000 
 TYR   0.007   0.001   TYR A 998 
 PHE   0.012   0.001   PHE A 843 
 TRP   0.008   0.001   TRP A 696 
 HIS   0.001   0.000   HIS A 781 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 2504)
  covalent geometry    : angle       0.48467 ( 3424)
  hydrogen bonds       : bond        0.03284 (  219)
  hydrogen bonds       : angle       3.35471 (  651)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.071 
Fit side-chains
   revert: symmetry clash
REVERT: A  686 LYS cc_start: 0.8142 (tppt) cc_final: 0.7763 (mmmm)
  outliers start: 3
  outliers final: 3
  residues processed: 43
  average time/residue: 0.0426
  time to fit residues: 2.3165
Evaluate side-chains
  45 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue  696 TRP
Chi-restraints excluded: chain A residue  991 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 11 optimal weight:   20.0000
   chunk 4 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 37 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 = 0.3943 r_free = 0.3943 target = 0.097659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.077934 restraints weight = 10066.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.079346 restraints weight = 7144.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.080074 restraints weight = 5715.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.080782 restraints weight = 5032.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.081248 restraints weight = 4578.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          1.0126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2504  Z= 0.155
  Angle     :  0.551   6.025   3424  Z= 0.290
  Chirality :  0.036   0.109    417
  Planarity :  0.003   0.026    452
  Dihedral  :  3.542  15.346    406
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 22.31 %
    Favored  : 75.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.89 (0.44), residues: 383
  helix:  2.54 (0.29), residues: 298
  sheet:  None (None), residues: 0
  loop : -0.43 (0.75), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 764 
 TYR   0.011   0.002   TYR A1044 
 PHE   0.012   0.002   PHE A 843 
 TRP   0.034   0.003   TRP A1048 
 HIS   0.001   0.001   HIS A 781 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 2504)
  covalent geometry    : angle       0.55136 ( 3424)
  hydrogen bonds       : bond        0.04047 (  219)
  hydrogen bonds       : angle       3.75798 (  651)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.058 
Fit side-chains
REVERT: A  686 LYS cc_start: 0.8203 (tppt) cc_final: 0.7804 (mmmm)
  outliers start: 3
  outliers final: 3
  residues processed: 39
  average time/residue: 0.0481
  time to fit residues: 2.3887
Evaluate side-chains
  40 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  991 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0970
   chunk 31 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.098817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.079065 restraints weight = 10105.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.080599 restraints weight = 7121.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.081415 restraints weight = 5704.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.082132 restraints weight = 5031.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.082581 restraints weight = 4549.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          1.0158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   2504  Z= 0.106
  Angle     :  0.517   8.105   3424  Z= 0.266
  Chirality :  0.035   0.149    417
  Planarity :  0.003   0.032    452
  Dihedral  :  3.230  13.282    406
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 24.62 %
    Favored  : 73.85 %
  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:  3.39 (0.44), residues: 383
  helix:  2.85 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.11 (0.77), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 764 
 TYR   0.005   0.001   TYR A1044 
 PHE   0.012   0.001   PHE A 843 
 TRP   0.009   0.001   TRP A 696 
 HIS   0.001   0.000   HIS A 781 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 2504)
  covalent geometry    : angle       0.51700 ( 3424)
  hydrogen bonds       : bond        0.03205 (  219)
  hydrogen bonds       : angle       3.38231 (  651)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A  686 LYS cc_start: 0.8088 (tppt) cc_final: 0.7724 (mmmm)
REVERT: A  982 HIS cc_start: 0.7526 (m-70) cc_final: 0.7212 (m-70)
REVERT: A  985 GLN cc_start: 0.6716 (mp10) cc_final: 0.5833 (mm-40)
  outliers start: 2
  outliers final: 1
  residues processed: 40
  average time/residue: 0.0485
  time to fit residues: 2.4475
Evaluate side-chains
  39 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 11 optimal weight:   20.0000
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 608 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 = 0.3938 r_free = 0.3938 target = 0.097367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.077392 restraints weight = 9957.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.078777 restraints weight = 7183.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.079762 restraints weight = 5770.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.080202 restraints weight = 5031.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.080596 restraints weight = 4673.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          1.0345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2504  Z= 0.138
  Angle     :  0.547   8.512   3424  Z= 0.283
  Chirality :  0.036   0.133    417
  Planarity :  0.003   0.032    452
  Dihedral  :  3.414  14.262    406
  Min Nonbonded Distance : 2.662

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 22.31 %
    Favored  : 75.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.19 (0.44), residues: 383
  helix:  2.68 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.07 (0.78), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 764 
 TYR   0.009   0.001   TYR A1044 
 PHE   0.011   0.001   PHE A 843 
 TRP   0.011   0.002   TRP A 696 
 HIS   0.002   0.001   HIS A 906 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 2504)
  covalent geometry    : angle       0.54738 ( 3424)
  hydrogen bonds       : bond        0.03614 (  219)
  hydrogen bonds       : angle       3.56332 (  651)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 564.08 seconds
wall clock time: 10 minutes 18.00 seconds (618.00 seconds total)