Starting phenix.real_space_refine
on Mon Feb 10 20:53:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8edl_28035/02_2025/8edl_28035.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8edl_28035/02_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_28035/02_2025/8edl_28035.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8edl_28035/02_2025/8edl_28035.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8edl_28035/02_2025/8edl_28035.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8edl_28035/02_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-5592/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: 2.38, per 1000 atoms: 0.96
  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: 0.50
  Conformation dependent library (CDL) restraints added in 341.9 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: 0.65

  Time building geometry restraints manager: 0.60 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:             0.690
  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:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.040
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.880
-------------------------------------------------------------------------------
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= 0.141
  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 

*********************** 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  : 0.291 
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: 0.1764
  time to fit residues: 13.9829
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 = 43)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.089644 restraints weight = 9778.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.091280 restraints weight = 6849.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.092362 restraints weight = 5392.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
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= 0.160
  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 

*********************** 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  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.7474 (OUTLIER) cc_final: 0.7172 (p)
REVERT: A  985 GLN cc_start: 0.5147 (mp10) cc_final: 0.4317 (mm-40)
REVERT: A 1041 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7021 (tpp)
REVERT: A 1085 LEU cc_start: 0.7735 (mt) cc_final: 0.7488 (mp)
  outliers start: 5
  outliers final: 1
  residues processed: 54
  average time/residue: 0.1769
  time to fit residues: 11.2142
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  : 0.327 
-------------------------------------------------------------------------------
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:    0.9990
   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:    1.1988

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.102368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.082040 restraints weight = 9992.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.083509 restraints weight = 7188.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.084442 restraints weight = 5842.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.7180

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= 0.208
  Angle     :  0.542   7.000   3424  Z= 0.294
  Chirality :  0.035   0.108    417
  Planarity :  0.004   0.030    452
  Dihedral  :  3.531  17.165    406
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.35 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 17.69 %
    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:  2.73 (0.43), residues: 383
  helix:  2.47 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.73 (0.69), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 777 
 HIS   0.004   0.001   HIS A 982 
 PHE   0.012   0.002   PHE A 843 
 TYR   0.014   0.003   TYR A 998 
 ARG   0.005   0.001   ARG A 997 

*********************** 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
  52 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.7754 (t) cc_final: 0.7503 (p)
REVERT: A  594 THR cc_start: 0.9002 (p) cc_final: 0.8800 (p)
REVERT: A  686 LYS cc_start: 0.8401 (tppt) cc_final: 0.8050 (mmmm)
REVERT: A 1085 LEU cc_start: 0.8107 (mt) cc_final: 0.7846 (mp)
  outliers start: 6
  outliers final: 2
  residues processed: 48
  average time/residue: 0.1080
  time to fit residues: 6.6241
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  : 0.292 
-------------------------------------------------------------------------------
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 35 optimal weight:    0.0070
   chunk 37 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.7604

-------------------------------------------------------------------------------
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 = 0.4045 r_free = 0.4045 target = 0.103065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.082507 restraints weight = 9864.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.083982 restraints weight = 7090.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.084752 restraints weight = 5750.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.7582

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= 0.134
  Angle     :  0.448   4.948   3424  Z= 0.243
  Chirality :  0.034   0.109    417
  Planarity :  0.003   0.025    452
  Dihedral  :  3.246  14.283    406
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 21.54 %
    Favored  : 76.92 %
  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:  3.26 (0.44), residues: 383
  helix:  2.81 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.36 (0.71), residues: 84

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   0.013   0.002   PHE A 843 
 TYR   0.005   0.001   TYR A 692 
 ARG   0.003   0.000   ARG A1000 

*********************** 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: 2
    poor density    : 44
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.7849 (t) cc_final: 0.7567 (p)
REVERT: A  686 LYS cc_start: 0.8279 (tppt) cc_final: 0.8030 (tppt)
REVERT: A  985 GLN cc_start: 0.5901 (mp10) cc_final: 0.4535 (mm-40)
REVERT: A 1085 LEU cc_start: 0.8099 (mt) cc_final: 0.7852 (mp)
  outliers start: 2
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1168
  time to fit residues: 6.5718
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  : 0.299 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0270
   chunk 27 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.4976

-------------------------------------------------------------------------------
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 = 0.103460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.082092 restraints weight = 9888.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.083695 restraints weight = 7025.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.084554 restraints weight = 5643.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.7898

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= 0.116
  Angle     :  0.412   5.870   3424  Z= 0.224
  Chirality :  0.033   0.108    417
  Planarity :  0.002   0.023    452
  Dihedral  :  2.997  13.015    406
  Min Nonbonded Distance : 2.675

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 20.00 %
    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:  3.59 (0.44), residues: 383
  helix:  3.03 (0.30), residues: 298
  sheet:  None (None), residues: 0
  loop : -0.14 (0.70), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 696 
 HIS   0.001   0.000   HIS A 781 
 PHE   0.013   0.001   PHE A 843 
 TYR   0.003   0.001   TYR A 998 
 ARG   0.002   0.000   ARG A 997 

*********************** 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
  48 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.7734 (t) cc_final: 0.7403 (p)
REVERT: A  686 LYS cc_start: 0.8194 (tppt) cc_final: 0.7968 (tppt)
REVERT: A 1041 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6756 (mmt)
REVERT: A 1085 LEU cc_start: 0.8101 (mt) cc_final: 0.7780 (mp)
  outliers start: 5
  outliers final: 2
  residues processed: 44
  average time/residue: 0.1016
  time to fit residues: 5.7012
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  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue  904 CYS
Chi-restraints excluded: chain A residue 1041 MET
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:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3984 r_free = 0.3984 target = 0.099877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.079141 restraints weight = 9955.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.080522 restraints weight = 7125.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.081447 restraints weight = 5792.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.8889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2504  Z= 0.189
  Angle     :  0.486   5.629   3424  Z= 0.266
  Chirality :  0.035   0.128    417
  Planarity :  0.003   0.034    452
  Dihedral  :  3.398  14.976    406
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 6.55
  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 (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:  3.10 (0.43), residues: 383
  helix:  2.67 (0.29), residues: 298
  sheet:  None (None), residues: 0
  loop : -0.28 (0.72), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 837 
 HIS   0.003   0.001   HIS A 982 
 PHE   0.011   0.002   PHE A1037 
 TYR   0.009   0.001   TYR A 998 
 ARG   0.004   0.001   ARG A1000 

*********************** 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
  48 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.8056 (t) cc_final: 0.7782 (p)
REVERT: A  686 LYS cc_start: 0.8359 (tppt) cc_final: 0.7900 (mmmt)
REVERT: A 1085 LEU cc_start: 0.8296 (mt) cc_final: 0.7972 (mp)
  outliers start: 3
  outliers final: 1
  residues processed: 46
  average time/residue: 0.1635
  time to fit residues: 8.9916
Evaluate side-chains
  44 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0980
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4011 r_free = 0.4011 target = 0.100909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.080621 restraints weight = 10301.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.082076 restraints weight = 7175.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.082853 restraints weight = 5765.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.9148

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= 0.135
  Angle     :  0.433   4.071   3424  Z= 0.238
  Chirality :  0.034   0.134    417
  Planarity :  0.003   0.024    452
  Dihedral  :  3.130  13.696    406
  Min Nonbonded Distance : 2.674

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 22.31 %
    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:  3.39 (0.43), residues: 383
  helix:  2.84 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.06 (0.72), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1048 
 HIS   0.001   0.000   HIS A 982 
 PHE   0.011   0.001   PHE A 843 
 TYR   0.006   0.001   TYR A1044 
 ARG   0.006   0.001   ARG A1000 

*********************** 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
  47 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.8025 (t) cc_final: 0.7708 (p)
REVERT: A  686 LYS cc_start: 0.8244 (tppt) cc_final: 0.8014 (tppt)
REVERT: A 1044 TYR cc_start: 0.7590 (m-10) cc_final: 0.7165 (m-10)
REVERT: A 1085 LEU cc_start: 0.8209 (mt) cc_final: 0.7849 (mp)
  outliers start: 2
  outliers final: 1
  residues processed: 46
  average time/residue: 0.1414
  time to fit residues: 7.9191
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  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 4 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4006 r_free = 0.4006 target = 0.100617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.079927 restraints weight = 9939.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.081367 restraints weight = 7088.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.082256 restraints weight = 5739.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.9301

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= 0.147
  Angle     :  0.495   7.911   3424  Z= 0.260
  Chirality :  0.034   0.133    417
  Planarity :  0.003   0.023    452
  Dihedral  :  3.128  13.127    406
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 23.08 %
    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:  3.48 (0.44), residues: 383
  helix:  2.87 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop :  0.06 (0.75), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1048 
 HIS   0.001   0.000   HIS A 781 
 PHE   0.011   0.001   PHE A 843 
 TYR   0.007   0.001   TYR A 998 
 ARG   0.004   0.001   ARG A1000 

*********************** 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
  43 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.8074 (t) cc_final: 0.7723 (p)
REVERT: A  686 LYS cc_start: 0.8297 (tppt) cc_final: 0.8068 (tppt)
REVERT: A 1085 LEU cc_start: 0.8202 (mt) cc_final: 0.7890 (mp)
  outliers start: 1
  outliers final: 1
  residues processed: 42
  average time/residue: 0.1320
  time to fit residues: 6.8226
Evaluate side-chains
  42 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  693 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0370
   chunk 9 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 37 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.7460

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.100687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.080142 restraints weight = 9952.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.081581 restraints weight = 7118.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.082502 restraints weight = 5754.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.9497

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= 0.144
  Angle     :  0.504   6.885   3424  Z= 0.267
  Chirality :  0.035   0.132    417
  Planarity :  0.003   0.025    452
  Dihedral  :  3.100  12.956    406
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  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 (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:  3.57 (0.44), residues: 383
  helix:  2.93 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop :  0.14 (0.74), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1048 
 HIS   0.001   0.000   HIS A 781 
 PHE   0.026   0.002   PHE A1037 
 TYR   0.009   0.001   TYR A1044 
 ARG   0.004   0.001   ARG A1000 

*********************** 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
  46 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 SER cc_start: 0.8036 (t) cc_final: 0.7677 (p)
REVERT: A  686 LYS cc_start: 0.8302 (tppt) cc_final: 0.8074 (tppt)
REVERT: A 1085 LEU cc_start: 0.8271 (mt) cc_final: 0.7964 (mp)
  outliers start: 2
  outliers final: 1
  residues processed: 44
  average time/residue: 0.1319
  time to fit residues: 7.1411
Evaluate side-chains
  42 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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 5 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0770
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   overall best weight:    1.0540

-------------------------------------------------------------------------------
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 = 0.3976 r_free = 0.3976 target = 0.099425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.079092 restraints weight = 9890.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.080535 restraints weight = 7100.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.081258 restraints weight = 5761.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.9904

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= 0.166
  Angle     :  0.531   6.049   3424  Z= 0.281
  Chirality :  0.035   0.140    417
  Planarity :  0.003   0.030    452
  Dihedral  :  3.274  13.794    406
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  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:  3.35 (0.43), residues: 383
  helix:  2.83 (0.29), residues: 296
  sheet:  None (None), residues: 0
  loop : -0.01 (0.71), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A1048 
 HIS   0.004   0.001   HIS A 982 
 PHE   0.029   0.002   PHE A1037 
 TYR   0.008   0.001   TYR A 998 
 ARG   0.003   0.001   ARG A 607 

********************** 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
  43 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  686 LYS cc_start: 0.8317 (tppt) cc_final: 0.8077 (tppt)
REVERT: A 1085 LEU cc_start: 0.8227 (mt) cc_final: 0.7965 (mp)
  outliers start: 1
  outliers final: 1
  residues processed: 42
  average time/residue: 0.1358
  time to fit residues: 6.9864
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  : 0.266 
-------------------------------------------------------------------------------
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 25 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 36 optimal weight:    9.9990
   chunk 26 optimal weight:    0.5980
   chunk 37 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.099652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.079222 restraints weight = 9937.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.080699 restraints weight = 7113.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.081370 restraints weight = 5745.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          1.0040

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= 0.163
  Angle     :  0.519   6.124   3424  Z= 0.280
  Chirality :  0.035   0.127    417
  Planarity :  0.003   0.028    452
  Dihedral  :  3.230  13.155    406
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.09
  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 (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:  3.39 (0.44), residues: 383
  helix:  2.87 (0.29), residues: 296
  sheet:  None (None), residues: 0
  loop : -0.05 (0.71), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A1048 
 HIS   0.002   0.001   HIS A 982 
 PHE   0.031   0.002   PHE A1037 
 TYR   0.017   0.002   TYR A1044 
 ARG   0.003   0.001   ARG A 607 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1081.34 seconds
wall clock time: 19 minutes 58.94 seconds (1198.94 seconds total)