Starting phenix.real_space_refine
on Wed Jul 23 08:33:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8edl_28035/07_2025/8edl_28035.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8edl_28035/07_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_28035/07_2025/8edl_28035.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8edl_28035/07_2025/8edl_28035.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8edl_28035/07_2025/8edl_28035.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8edl_28035/07_2025/8edl_28035.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 15, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 16, 'ASP:plan': 19, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 317
  Time building chain proxies: 2.94, per 1000 atoms: 1.19
  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: 0.70
  Conformation dependent library (CDL) restraints added in 386.3 milliseconds
  

  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: 0.27
  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: 0.84

  Time building geometry restraints manager: 0.85 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:             1.890
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.720
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.760
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.009   0.002   TRP A 696 
 HIS   0.001   0.001   HIS A 906 
 PHE   0.029   0.002   PHE A1037 
 TYR   0.005   0.001   TYR A1044 
 ARG   0.002   0.001   ARG A 765 

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

*********************** 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  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A 1037 PHE cc_start: 0.7781 (t80) cc_final: 0.7534 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1807
  time to fit residues: 14.3034
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  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0570
   chunk 18 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   overall best weight:    0.7098

-------------------------------------------------------------------------------
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 = 0.4099 r_free = 0.4099 target = 0.108353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.089635 restraints weight = 9778.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.091291 restraints weight = 6820.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.092258 restraints weight = 5371.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.4180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2504  Z= 0.122
  Angle     :  0.513   7.241   3424  Z= 0.267
  Chirality :  0.035   0.129    417
  Planarity :  0.004   0.039    452
  Dihedral  :  3.362  15.098    406
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 6.55
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.02 (0.44), residues: 383
  helix:  2.63 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.44 (0.75), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 837 
 HIS   0.006   0.001   HIS A 781 
 PHE   0.007   0.002   PHE A 945 
 TYR   0.011   0.002   TYR A 998 
 ARG   0.004   0.001   ARG A1038 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03583 (  219)
  hydrogen bonds       : angle       3.41918 (  651)
  covalent geometry    : bond        0.00243 ( 2504)
  covalent geometry    : angle       0.51337 ( 3424)

*********************** 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  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.7468 (OUTLIER) cc_final: 0.7166 (p)
REVERT: A  985 GLN cc_start: 0.5117 (mp10) cc_final: 0.4288 (mm-40)
REVERT: A 1041 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.7027 (tpp)
REVERT: A 1085 LEU cc_start: 0.7735 (mt) cc_final: 0.7489 (mp)
  outliers start: 5
  outliers final: 1
  residues processed: 54
  average time/residue: 0.1562
  time to fit residues: 9.9503
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  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  587 SER
Chi-restraints excluded: chain A residue  904 CYS
Chi-restraints excluded: chain A residue 1041 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.102807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.082616 restraints weight = 9952.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.084118 restraints weight = 7146.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.085075 restraints weight = 5767.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.6820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2504  Z= 0.146
  Angle     :  0.528   6.617   3424  Z= 0.285
  Chirality :  0.035   0.106    417
  Planarity :  0.003   0.028    452
  Dihedral  :  3.435  16.712    406
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.09 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.23 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.43), residues: 383
  helix:  2.55 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.69 (0.69), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 777 
 HIS   0.005   0.001   HIS A 982 
 PHE   0.013   0.002   PHE A 843 
 TYR   0.013   0.003   TYR A 998 
 ARG   0.004   0.001   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04251 (  219)
  hydrogen bonds       : angle       3.64564 (  651)
  covalent geometry    : bond        0.00300 ( 2504)
  covalent geometry    : angle       0.52784 ( 3424)

*********************** 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
  46 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.7619 (t) cc_final: 0.7330 (p)
REVERT: A  686 LYS cc_start: 0.8396 (tppt) cc_final: 0.8115 (mmmm)
REVERT: A 1085 LEU cc_start: 0.8046 (mt) cc_final: 0.7793 (mp)
  outliers start: 4
  outliers final: 1
  residues processed: 44
  average time/residue: 0.1007
  time to fit residues: 5.8003
Evaluate side-chains
  43 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 35 optimal weight:    0.0670
   chunk 37 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    0.1980
   chunk 2 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.6320

-------------------------------------------------------------------------------
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 = 0.4054 r_free = 0.4054 target = 0.104093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.083334 restraints weight = 9904.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.084836 restraints weight = 7120.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.085627 restraints weight = 5771.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.7222

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= 0.097
  Angle     :  0.443   5.247   3424  Z= 0.239
  Chirality :  0.033   0.109    417
  Planarity :  0.003   0.024    452
  Dihedral  :  3.170  13.925    406
  Min Nonbonded Distance : 2.675

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 21.54 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.43 (0.44), residues: 383
  helix:  2.92 (0.30), residues: 298
  sheet:  None (None), residues: 0
  loop : -0.23 (0.70), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 837 
 HIS   0.003   0.001   HIS A 982 
 PHE   0.014   0.002   PHE A 843 
 TYR   0.004   0.001   TYR A 692 
 ARG   0.002   0.000   ARG A1000 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03173 (  219)
  hydrogen bonds       : angle       3.19819 (  651)
  covalent geometry    : bond        0.00192 ( 2504)
  covalent geometry    : angle       0.44258 ( 3424)

*********************** 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: 1
    poor density    : 45
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.7775 (t) cc_final: 0.7454 (p)
REVERT: A  686 LYS cc_start: 0.8319 (tppt) cc_final: 0.8072 (tppt)
REVERT: A  985 GLN cc_start: 0.5863 (mp10) cc_final: 0.4502 (mm-40)
REVERT: A 1041 MET cc_start: 0.7541 (tpp) cc_final: 0.6941 (tpp)
REVERT: A 1085 LEU cc_start: 0.8056 (mt) cc_final: 0.7804 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0951
  time to fit residues: 5.7366
Evaluate side-chains
  41 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    0.0000
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 35 optimal weight:    0.3980
   chunk 27 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.5384

-------------------------------------------------------------------------------
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 = 0.4050 r_free = 0.4050 target = 0.103253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.082507 restraints weight = 9954.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.083897 restraints weight = 7015.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.085056 restraints weight = 5691.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.7735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   2504  Z= 0.088
  Angle     :  0.404   4.590   3424  Z= 0.221
  Chirality :  0.033   0.107    417
  Planarity :  0.002   0.023    452
  Dihedral  :  2.941  13.107    406
  Min Nonbonded Distance : 2.676

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.77 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.70 (0.44), residues: 383
  helix:  3.09 (0.30), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.05 (0.71), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 696 
 HIS   0.001   0.000   HIS A 712 
 PHE   0.013   0.001   PHE A 843 
 TYR   0.005   0.001   TYR A 998 
 ARG   0.002   0.000   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02919 (  219)
  hydrogen bonds       : angle       3.05828 (  651)
  covalent geometry    : bond        0.00171 ( 2504)
  covalent geometry    : angle       0.40444 ( 3424)

*********************** 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
  50 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.7731 (t) cc_final: 0.7411 (p)
REVERT: A  686 LYS cc_start: 0.8222 (tppt) cc_final: 0.7997 (tppt)
REVERT: A 1085 LEU cc_start: 0.8086 (mt) cc_final: 0.7804 (mp)
  outliers start: 4
  outliers final: 1
  residues processed: 47
  average time/residue: 0.1377
  time to fit residues: 7.9054
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  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 30 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 786 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 = 0.3920 r_free = 0.3920 target = 0.096718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.076347 restraints weight = 10141.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.077618 restraints weight = 7307.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.078311 restraints weight = 5944.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.9467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2504  Z= 0.257
  Angle     :  0.641   9.016   3424  Z= 0.355
  Chirality :  0.039   0.149    417
  Planarity :  0.004   0.033    452
  Dihedral  :  4.216  15.875    406
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.31 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.42), residues: 383
  helix:  1.94 (0.29), residues: 294
  sheet:  None (None), residues: 0
  loop : -0.98 (0.68), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP A 837 
 HIS   0.002   0.001   HIS A 588 
 PHE   0.015   0.003   PHE A 710 
 TYR   0.015   0.002   TYR A 998 
 ARG   0.006   0.001   ARG A1000 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05404 (  219)
  hydrogen bonds       : angle       4.36788 (  651)
  covalent geometry    : bond        0.00515 ( 2504)
  covalent geometry    : angle       0.64056 ( 3424)

*********************** 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
  50 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  686 LYS cc_start: 0.8328 (tppt) cc_final: 0.7849 (mmmt)
REVERT: A 1044 TYR cc_start: 0.7995 (m-10) cc_final: 0.7790 (m-10)
REVERT: A 1085 LEU cc_start: 0.8336 (mt) cc_final: 0.8105 (mp)
  outliers start: 4
  outliers final: 2
  residues processed: 48
  average time/residue: 0.1503
  time to fit residues: 8.6451
Evaluate side-chains
  40 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  791 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 28 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 36 optimal weight:    9.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 786 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.099204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.078770 restraints weight = 10260.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.080202 restraints weight = 7409.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.081118 restraints weight = 5799.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.9517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   2504  Z= 0.110
  Angle     :  0.483   6.900   3424  Z= 0.260
  Chirality :  0.034   0.110    417
  Planarity :  0.003   0.033    452
  Dihedral  :  3.435  15.323    406
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 24.62 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.92 (0.43), residues: 383
  helix:  2.56 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.48 (0.72), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1048 
 HIS   0.001   0.000   HIS A 906 
 PHE   0.012   0.001   PHE A 843 
 TYR   0.005   0.001   TYR A 998 
 ARG   0.003   0.001   ARG A 914 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03472 (  219)
  hydrogen bonds       : angle       3.55632 (  651)
  covalent geometry    : bond        0.00226 ( 2504)
  covalent geometry    : angle       0.48296 ( 3424)

*********************** 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
  46 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  686 LYS cc_start: 0.8241 (tppt) cc_final: 0.7794 (mmmt)
REVERT: A 1044 TYR cc_start: 0.8010 (m-10) cc_final: 0.7785 (m-10)
REVERT: A 1085 LEU cc_start: 0.8191 (mt) cc_final: 0.7948 (mp)
  outliers start: 3
  outliers final: 2
  residues processed: 43
  average time/residue: 0.1426
  time to fit residues: 7.4307
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  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue  791 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0670
   chunk 5 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.3522

-------------------------------------------------------------------------------
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 = 0.3964 r_free = 0.3964 target = 0.098334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.077529 restraints weight = 9952.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.078925 restraints weight = 7226.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.079834 restraints weight = 5784.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.9771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2504  Z= 0.142
  Angle     :  0.556   7.330   3424  Z= 0.295
  Chirality :  0.036   0.167    417
  Planarity :  0.003   0.036    452
  Dihedral  :  3.490  14.518    406
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 24.62 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.43), residues: 383
  helix:  2.41 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.48 (0.73), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A1048 
 HIS   0.002   0.001   HIS A 982 
 PHE   0.012   0.002   PHE A1037 
 TYR   0.011   0.001   TYR A 998 
 ARG   0.004   0.001   ARG A1000 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04023 (  219)
  hydrogen bonds       : angle       3.74998 (  651)
  covalent geometry    : bond        0.00297 ( 2504)
  covalent geometry    : angle       0.55582 ( 3424)

*********************** 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: 4
    poor density    : 42
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  686 LYS cc_start: 0.8273 (tppt) cc_final: 0.7820 (mmmt)
REVERT: A  893 LYS cc_start: 0.6461 (mmtt) cc_final: 0.5921 (mptt)
REVERT: A 1044 TYR cc_start: 0.8080 (m-10) cc_final: 0.7856 (m-10)
  outliers start: 4
  outliers final: 4
  residues processed: 42
  average time/residue: 0.1268
  time to fit residues: 6.5314
Evaluate side-chains
  45 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue  993 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0370
   chunk 9 optimal weight:    8.9990
   chunk 26 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 36 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:   20.0000
   chunk 24 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.6858

-------------------------------------------------------------------------------
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**
A 793 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.099821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.080218 restraints weight = 10163.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.081742 restraints weight = 7160.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.082405 restraints weight = 5698.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.9893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   2504  Z= 0.106
  Angle     :  0.513   6.805   3424  Z= 0.268
  Chirality :  0.034   0.147    417
  Planarity :  0.003   0.033    452
  Dihedral  :  3.210  13.680    406
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 29.23 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.14 (0.44), residues: 383
  helix:  2.69 (0.30), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.29 (0.75), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1048 
 HIS   0.001   0.000   HIS A 906 
 PHE   0.014   0.002   PHE A1037 
 TYR   0.004   0.001   TYR A 998 
 ARG   0.002   0.000   ARG A 914 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03269 (  219)
  hydrogen bonds       : angle       3.37582 (  651)
  covalent geometry    : bond        0.00222 ( 2504)
  covalent geometry    : angle       0.51273 ( 3424)

*********************** 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
  48 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  686 LYS cc_start: 0.8246 (tppt) cc_final: 0.8016 (tppt)
REVERT: A  893 LYS cc_start: 0.6286 (mmtt) cc_final: 0.5904 (mptt)
REVERT: A 1044 TYR cc_start: 0.8171 (m-10) cc_final: 0.7804 (m-10)
  outliers start: 2
  outliers final: 1
  residues processed: 46
  average time/residue: 0.1338
  time to fit residues: 7.5414
Evaluate side-chains
  43 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  791 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0060
   chunk 6 optimal weight:    0.1980
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.8402

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.097045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.076389 restraints weight = 9940.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.077745 restraints weight = 7176.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.078649 restraints weight = 5788.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          1.0213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2504  Z= 0.173
  Angle     :  0.574   6.860   3424  Z= 0.310
  Chirality :  0.037   0.160    417
  Planarity :  0.003   0.033    452
  Dihedral  :  3.550  14.909    406
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 28.46 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.44), residues: 383
  helix:  2.34 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.49 (0.76), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A1048 
 HIS   0.002   0.001   HIS A 982 
 PHE   0.010   0.002   PHE A 843 
 TYR   0.011   0.002   TYR A 998 
 ARG   0.005   0.001   ARG A1000 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04280 (  219)
  hydrogen bonds       : angle       3.86610 (  651)
  covalent geometry    : bond        0.00360 ( 2504)
  covalent geometry    : angle       0.57446 ( 3424)

********************** 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
  44 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  686 LYS cc_start: 0.8302 (tppt) cc_final: 0.7978 (mmmm)
REVERT: A 1044 TYR cc_start: 0.8347 (m-10) cc_final: 0.7935 (m-10)
  outliers start: 3
  outliers final: 3
  residues processed: 41
  average time/residue: 0.1513
  time to fit residues: 7.5303
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  : 0.293 
-------------------------------------------------------------------------------
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 25 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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**
** A 793 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 = 0.3937 r_free = 0.3937 target = 0.097350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.077762 restraints weight = 10089.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.079199 restraints weight = 7172.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.080167 restraints weight = 5676.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          1.0376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2504  Z= 0.151
  Angle     :  0.579   9.544   3424  Z= 0.304
  Chirality :  0.036   0.147    417
  Planarity :  0.003   0.032    452
  Dihedral  :  3.483  14.389    406
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 31.54 %
    Favored  : 67.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.44), residues: 383
  helix:  2.35 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.56 (0.76), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A1048 
 HIS   0.003   0.001   HIS A 982 
 PHE   0.010   0.002   PHE A 843 
 TYR   0.010   0.001   TYR A 998 
 ARG   0.003   0.001   ARG A1000 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  219)
  hydrogen bonds       : angle       3.70324 (  651)
  covalent geometry    : bond        0.00316 ( 2504)
  covalent geometry    : angle       0.57926 ( 3424)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1166.92 seconds
wall clock time: 20 minutes 45.87 seconds (1245.87 seconds total)