Starting phenix.real_space_refine
on Wed Sep 17 03:15:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jex_36202/09_2025/8jex_36202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jex_36202/09_2025/8jex_36202.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jex_36202/09_2025/8jex_36202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jex_36202/09_2025/8jex_36202.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jex_36202/09_2025/8jex_36202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jex_36202/09_2025/8jex_36202.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1614      2.51       5
     N     450      2.21       5
     O     552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2616
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 377
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 377
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
    Chain: "J"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 45
          Classifications: {'peptide': 9}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'UNK:plan-1': 9}
          Unresolved non-hydrogen planarities: 9
    Chain: "H"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    P, G, B, K, A, Q, I, D, L, C
  Time building chain proxies: 0.48, per 1000 atoms: 0.18
  Number of scatterers: 2616
  At special positions: 0
  Unit cell: (112.05, 126.99, 31.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     552      8.00
     N     450      7.00
     C    1614      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
  Links applied
    NAG-SER
      " NAG A 201 " - " SER A  87 "
      " NAG B 201 " - " SER B  87 "
      " NAG G 201 " - " SER G  87 "
      " NAG H 201 " - " SER H  87 "
      " NAG K 201 " - " SER K  87 "
      " NAG P 201 " - " SER P  87 "
  Time building additional restraints: 0.29
  Conformation dependent library (CDL) restraints added in 174.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  660

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'H' and resid 40 through 44
    Processing sheet with id=AA2, first strand: chain 'H' and resid 50 through 51
      removed outlier: 6.458A  pdb=" N   HIS H  50 " --> pdb=" O   GLY P  51 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   HIS P  50 " --> pdb=" O   GLY G  51 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'H' and resid 63 through 66
    Processing sheet with id=AA4, first strand: chain 'H' and resid 70 through 72
    Processing sheet with id=AA5, first strand: chain 'H' and resid 76 through 79
      removed outlier: 6.453A  pdb=" N   ALA H  76 " --> pdb=" O   VAL P  77 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   GLN P  79 " --> pdb=" O   ALA H  76 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ALA H  78 " --> pdb=" O   GLN P  79 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ALA P  76 " --> pdb=" O   VAL G  77 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   GLN G  79 " --> pdb=" O   ALA P  76 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ALA P  78 " --> pdb=" O   GLN G  79 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 44
    Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 51
      removed outlier: 6.458A  pdb=" N   HIS B  50 " --> pdb=" O   GLY K  51 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   HIS K  50 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 66
    Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 72
    Processing sheet with id=AB1, first strand: chain 'B' and resid 76 through 79
      removed outlier: 6.452A  pdb=" N   ALA B  76 " --> pdb=" O   VAL K  77 " (cutoff:3.500A)
      removed outlier: 8.243A  pdb=" N   GLN K  79 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ALA B  78 " --> pdb=" O   GLN K  79 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   ALA K  76 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   GLN A  79 " --> pdb=" O   ALA K  76 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ALA K  78 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    36 hydrogen bonds defined for protein.
    108 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: 0.30

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.18 -     1.26: 468
        1.26 -     1.33: 113
        1.33 -     1.40: 355
        1.40 -     1.48: 468
        1.48 -     1.55: 1212
  Bond restraints: 2616
  Sorted by residual:
  bond pdb=" C7  NAG K 201 "
       pdb=" N2  NAG K 201 "
    ideal  model  delta    sigma   weight residual
    1.346  1.452 -0.106 2.00e-02 2.50e+03 2.83e+01
  bond pdb=" C7  NAG B 201 "
       pdb=" N2  NAG B 201 "
    ideal  model  delta    sigma   weight residual
    1.346  1.452 -0.106 2.00e-02 2.50e+03 2.83e+01
  bond pdb=" C7  NAG P 201 "
       pdb=" N2  NAG P 201 "
    ideal  model  delta    sigma   weight residual
    1.346  1.452 -0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" C7  NAG H 201 "
       pdb=" N2  NAG H 201 "
    ideal  model  delta    sigma   weight residual
    1.346  1.452 -0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" C7  NAG G 201 "
       pdb=" N2  NAG G 201 "
    ideal  model  delta    sigma   weight residual
    1.346  1.452 -0.106 2.00e-02 2.50e+03 2.81e+01
  ... (remaining 2611 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 3256
        1.70 -     3.40: 182
        3.40 -     5.10: 96
        5.10 -     6.80: 0
        6.80 -     8.51: 12
  Bond angle restraints: 3546
  Sorted by residual:
  angle pdb=" CB  HIS G  50 "
        pdb=" CG  HIS G  50 "
        pdb=" CD2 HIS G  50 "
      ideal   model   delta    sigma   weight residual
     131.20  122.69    8.51 1.30e+00 5.92e-01 4.28e+01
  angle pdb=" CB  HIS B  50 "
        pdb=" CG  HIS B  50 "
        pdb=" CD2 HIS B  50 "
      ideal   model   delta    sigma   weight residual
     131.20  122.71    8.49 1.30e+00 5.92e-01 4.27e+01
  angle pdb=" CB  HIS K  50 "
        pdb=" CG  HIS K  50 "
        pdb=" CD2 HIS K  50 "
      ideal   model   delta    sigma   weight residual
     131.20  122.71    8.49 1.30e+00 5.92e-01 4.26e+01
  angle pdb=" CB  HIS H  50 "
        pdb=" CG  HIS H  50 "
        pdb=" CD2 HIS H  50 "
      ideal   model   delta    sigma   weight residual
     131.20  122.73    8.47 1.30e+00 5.92e-01 4.24e+01
  angle pdb=" CB  HIS P  50 "
        pdb=" CG  HIS P  50 "
        pdb=" CD2 HIS P  50 "
      ideal   model   delta    sigma   weight residual
     131.20  122.74    8.46 1.30e+00 5.92e-01 4.24e+01
  ... (remaining 3541 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.32: 1320
        9.32 -    18.63: 138
       18.63 -    27.95: 90
       27.95 -    37.26: 42
       37.26 -    46.58: 12
  Dihedral angle restraints: 1602
    sinusoidal: 564
      harmonic: 1038
  Sorted by residual:
  dihedral pdb=" C   LYS G  45 "
           pdb=" N   LYS G  45 "
           pdb=" CA  LYS G  45 "
           pdb=" CB  LYS G  45 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.21    6.61     0      2.50e+00 1.60e-01 6.99e+00
  dihedral pdb=" C   LYS B  45 "
           pdb=" N   LYS B  45 "
           pdb=" CA  LYS B  45 "
           pdb=" CB  LYS B  45 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.19    6.59     0      2.50e+00 1.60e-01 6.95e+00
  dihedral pdb=" C   LYS P  45 "
           pdb=" N   LYS P  45 "
           pdb=" CA  LYS P  45 "
           pdb=" CB  LYS P  45 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.19    6.59     0      2.50e+00 1.60e-01 6.94e+00
  ... (remaining 1599 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 314
       0.044 -    0.089: 101
       0.089 -    0.133: 53
       0.133 -    0.178: 6
       0.178 -    0.222: 12
  Chirality restraints: 486
  Sorted by residual:
  chirality pdb=" CA  LYS B  45 "
            pdb=" N   LYS B  45 "
            pdb=" C   LYS B  45 "
            pdb=" CB  LYS B  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  LYS G  45 "
            pdb=" N   LYS G  45 "
            pdb=" C   LYS G  45 "
            pdb=" CB  LYS G  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  LYS P  45 "
            pdb=" N   LYS P  45 "
            pdb=" C   LYS P  45 "
            pdb=" CB  LYS P  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 483 not shown)

  Planarity restraints: 438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU G  83 "   -0.004 2.00e-02 2.50e+03   8.74e-03 7.64e-01
        pdb=" C   GLU G  83 "    0.015 2.00e-02 2.50e+03
        pdb=" O   GLU G  83 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   GLY G  84 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU P  83 "   -0.004 2.00e-02 2.50e+03   8.70e-03 7.56e-01
        pdb=" C   GLU P  83 "    0.015 2.00e-02 2.50e+03
        pdb=" O   GLU P  83 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   GLY P  84 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU K  83 "    0.004 2.00e-02 2.50e+03   8.57e-03 7.34e-01
        pdb=" C   GLU K  83 "   -0.015 2.00e-02 2.50e+03
        pdb=" O   GLU K  83 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLY K  84 "    0.005 2.00e-02 2.50e+03
  ... (remaining 435 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 1388
        2.98 -     3.46: 2214
        3.46 -     3.94: 3618
        3.94 -     4.42: 4179
        4.42 -     4.90: 8243
  Nonbonded interactions: 19642
  Sorted by model distance:
  nonbonded pdb=" O5  NAG B 201 "
            pdb=" O6  NAG B 201 "
     model   vdw
     2.505 2.432
  nonbonded pdb=" O5  NAG H 201 "
            pdb=" O6  NAG H 201 "
     model   vdw
     2.505 2.432
  nonbonded pdb=" O5  NAG G 201 "
            pdb=" O6  NAG G 201 "
     model   vdw
     2.505 2.432
  nonbonded pdb=" O5  NAG K 201 "
            pdb=" O6  NAG K 201 "
     model   vdw
     2.505 2.432
  nonbonded pdb=" O5  NAG P 201 "
            pdb=" O6  NAG P 201 "
     model   vdw
     2.506 2.432
  ... (remaining 19637 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'H'
  selection = chain 'P'
  selection = chain 'G'
  selection = chain 'B'
  selection = chain 'K'
  selection = chain 'A'
}
ncs_group {
  reference = chain 'J'
  selection = chain 'Q'
  selection = chain 'I'
  selection = chain 'D'
  selection = chain 'L'
  selection = chain 'C'
}

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 individual isotropic
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:             2.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     4.020
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
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      :  0.012   0.106   2622  Z= 0.712
  Angle     :  2.001  39.614   3558  Z= 0.891
  Chirality :  0.062   0.222    486
  Planarity :  0.002   0.009    438
  Dihedral  : 12.572  46.580    942
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.82 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.98 (0.27), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.79 (0.20), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR A  39 
 HIS   0.002   0.001   HIS K  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.01217 ( 2616)
  covalent geometry    : angle       1.13106 ( 3546)
  hydrogen bonds       : bond        0.18255 (   36)
  hydrogen bonds       : angle       7.56088 (  108)
  link_NAG-SER         : bond        0.02054 (    6)
  link_NAG-SER         : angle      28.43880 (   12)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.100 
Fit side-chains
REVERT: G   58 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8080 (mtpt)
REVERT: A   58 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8115 (mtpt)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0872
  time to fit residues: 4.5660
Evaluate side-chains
  45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 = 0.4247 r_free = 0.4247 target = 0.132736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.105634 restraints weight = 3702.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 3.35
r_work: 0.3784 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   2622  Z= 0.208
  Angle     :  0.617   4.438   3558  Z= 0.308
  Chirality :  0.051   0.116    486
  Planarity :  0.002   0.008    438
  Dihedral  :  6.531  29.644    504
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 15.38 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.46 (0.30), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.23), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR P  39 
 HIS   0.001   0.000   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 2616)
  covalent geometry    : angle       0.58648 ( 3546)
  hydrogen bonds       : bond        0.01869 (   36)
  hydrogen bonds       : angle       4.38300 (  108)
  link_NAG-SER         : bond        0.00076 (    6)
  link_NAG-SER         : angle       3.35560 (   12)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.096 
Fit side-chains
REVERT: H   43 LYS cc_start: 0.8857 (mptt) cc_final: 0.8509 (mtmm)
REVERT: H   58 LYS cc_start: 0.8365 (ttmt) cc_final: 0.8082 (mtpt)
REVERT: B   43 LYS cc_start: 0.8828 (mptt) cc_final: 0.8453 (mtmm)
REVERT: A   58 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8218 (mtpt)
  outliers start: 2
  outliers final: 2
  residues processed: 45
  average time/residue: 0.0854
  time to fit residues: 4.4101
Evaluate side-chains
  45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain G residue   59 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 25 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0470
   chunk 1 optimal weight:    7.9990
   chunk 10 optimal weight:    0.7980
   chunk 16 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.6482

-------------------------------------------------------------------------------
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 = 0.4241 r_free = 0.4241 target = 0.131835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.104850 restraints weight = 3735.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 3.40
r_work: 0.3773 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2622  Z= 0.169
  Angle     :  0.528   3.459   3558  Z= 0.272
  Chirality :  0.049   0.112    486
  Planarity :  0.002   0.007    438
  Dihedral  :  3.774  11.585    504
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.09 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.12 (0.34), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.26), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR K  39 
 HIS   0.001   0.000   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 2616)
  covalent geometry    : angle       0.50789 ( 3546)
  hydrogen bonds       : bond        0.01718 (   36)
  hydrogen bonds       : angle       4.09410 (  108)
  link_NAG-SER         : bond        0.00721 (    6)
  link_NAG-SER         : angle       2.55099 (   12)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.095 
Fit side-chains
REVERT: H   58 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8022 (mtpp)
REVERT: B   43 LYS cc_start: 0.8803 (mptt) cc_final: 0.8479 (mtmm)
  outliers start: 7
  outliers final: 6
  residues processed: 36
  average time/residue: 0.0916
  time to fit residues: 3.7545
Evaluate side-chains
  42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain P residue   59 THR
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain A residue   59 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 3 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.4242 r_free = 0.4242 target = 0.131683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.105291 restraints weight = 3701.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 3.35
r_work: 0.3779 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2622  Z= 0.140
  Angle     :  0.463   3.363   3558  Z= 0.244
  Chirality :  0.049   0.113    486
  Planarity :  0.001   0.007    438
  Dihedral  :  3.521  11.834    504
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 18.80 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.80 (0.37), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.28), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR P  39 
 HIS   0.001   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 2616)
  covalent geometry    : angle       0.45451 ( 3546)
  hydrogen bonds       : bond        0.01216 (   36)
  hydrogen bonds       : angle       4.06780 (  108)
  link_NAG-SER         : bond        0.00468 (    6)
  link_NAG-SER         : angle       1.62567 (   12)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.092 
Fit side-chains
REVERT: H   58 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7989 (mtpp)
  outliers start: 11
  outliers final: 11
  residues processed: 40
  average time/residue: 0.0722
  time to fit residues: 3.4135
Evaluate side-chains
  45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   37 VAL
Chi-restraints excluded: chain P residue   59 THR
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain K residue   37 VAL
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   59 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.9388

-------------------------------------------------------------------------------
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 = 0.4252 r_free = 0.4252 target = 0.131886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.105043 restraints weight = 3635.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 3.26
r_work: 0.3762 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   2622  Z= 0.184
  Angle     :  0.517   3.905   3558  Z= 0.269
  Chirality :  0.049   0.114    486
  Planarity :  0.002   0.005    438
  Dihedral  :  3.801  12.119    504
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 1.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 20.09 %
    Favored  : 74.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.65 (0.38), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.29), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR P  39 
 HIS   0.001   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 2616)
  covalent geometry    : angle       0.50784 ( 3546)
  hydrogen bonds       : bond        0.01335 (   36)
  hydrogen bonds       : angle       3.92776 (  108)
  link_NAG-SER         : bond        0.00727 (    6)
  link_NAG-SER         : angle       1.76727 (   12)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 34
  time to evaluate  : 0.106 
Fit side-chains
REVERT: H   58 LYS cc_start: 0.8363 (ttmt) cc_final: 0.8080 (mtpp)
  outliers start: 13
  outliers final: 12
  residues processed: 41
  average time/residue: 0.0697
  time to fit residues: 3.3936
Evaluate side-chains
  45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain P residue   37 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain K residue   37 VAL
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   59 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.4219 r_free = 0.4219 target = 0.129703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.102820 restraints weight = 3683.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 3.31
r_work: 0.3730 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.3230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.023   2622  Z= 0.260
  Angle     :  0.609   4.826   3558  Z= 0.315
  Chirality :  0.051   0.112    486
  Planarity :  0.002   0.005    438
  Dihedral  :  4.223  13.183    504
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 21.37 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.64 (0.39), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.30), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR P  39 
 HIS   0.001   0.001   HIS K  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 2616)
  covalent geometry    : angle       0.60018 ( 3546)
  hydrogen bonds       : bond        0.01579 (   36)
  hydrogen bonds       : angle       3.81500 (  108)
  link_NAG-SER         : bond        0.00949 (    6)
  link_NAG-SER         : angle       1.83405 (   12)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 35
  time to evaluate  : 0.098 
Fit side-chains
REVERT: H   58 LYS cc_start: 0.8326 (ttmt) cc_final: 0.8081 (mtpp)
REVERT: B   58 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8170 (mtpt)
  outliers start: 14
  outliers final: 14
  residues processed: 43
  average time/residue: 0.0774
  time to fit residues: 3.9127
Evaluate side-chains
  49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 35
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   42 SER
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain P residue   37 VAL
Chi-restraints excluded: chain P residue   59 THR
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain K residue   37 VAL
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   59 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 17 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0980
   chunk 25 optimal weight:   10.0000
   chunk 6 optimal weight:    0.5980
   chunk 23 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 4 optimal weight:    0.5980
   chunk 28 optimal weight:    6.9990
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.137460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.110921 restraints weight = 3434.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 3.16
r_work: 0.3876 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.007   2622  Z= 0.065
  Angle     :  0.352   3.267   3558  Z= 0.198
  Chirality :  0.048   0.116    486
  Planarity :  0.001   0.005    438
  Dihedral  :  3.091   9.424    504
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 26.50 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.35 (0.41), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.55 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR A  39 
 HIS   0.002   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00131 ( 2616)
  covalent geometry    : angle       0.35109 ( 3546)
  hydrogen bonds       : bond        0.00780 (   36)
  hydrogen bonds       : angle       3.51730 (  108)
  link_NAG-SER         : bond        0.00199 (    6)
  link_NAG-SER         : angle       0.57516 (   12)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.094 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 33
  average time/residue: 0.0917
  time to fit residues: 3.5657
Evaluate side-chains
  33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 26 optimal weight:    0.2980
   chunk 16 optimal weight:    8.9990
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    3.4386

-------------------------------------------------------------------------------
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 = 0.4239 r_free = 0.4239 target = 0.130899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.104136 restraints weight = 3636.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 3.26
r_work: 0.3757 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.018   2622  Z= 0.210
  Angle     :  0.522   4.012   3558  Z= 0.272
  Chirality :  0.049   0.114    486
  Planarity :  0.002   0.004    438
  Dihedral  :  3.767  12.116    504
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 24.79 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.34 (0.41), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR P  39 
 HIS   0.002   0.001   HIS K  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 2616)
  covalent geometry    : angle       0.51561 ( 3546)
  hydrogen bonds       : bond        0.01284 (   36)
  hydrogen bonds       : angle       3.58919 (  108)
  link_NAG-SER         : bond        0.00781 (    6)
  link_NAG-SER         : angle       1.49532 (   12)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.096 
Fit side-chains
REVERT: H   58 LYS cc_start: 0.8352 (ttmt) cc_final: 0.8063 (mtpp)
  outliers start: 6
  outliers final: 6
  residues processed: 37
  average time/residue: 0.0745
  time to fit residues: 3.2821
Evaluate side-chains
  39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain K residue   37 VAL
Chi-restraints excluded: chain A residue   59 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 6 optimal weight:    0.3980
   chunk 25 optimal weight:    9.9990
   chunk 27 optimal weight:    4.9990
   chunk 23 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   overall best weight:    3.6788

-------------------------------------------------------------------------------
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 = 0.4229 r_free = 0.4229 target = 0.130456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.103429 restraints weight = 3713.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 3.28
r_work: 0.3740 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.020   2622  Z= 0.226
  Angle     :  0.547   4.183   3558  Z= 0.287
  Chirality :  0.050   0.115    486
  Planarity :  0.002   0.005    438
  Dihedral  :  3.957  12.495    504
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 24.79 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.40 (0.40), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR K  39 
 HIS   0.001   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 2616)
  covalent geometry    : angle       0.54094 ( 3546)
  hydrogen bonds       : bond        0.01360 (   36)
  hydrogen bonds       : angle       3.58529 (  108)
  link_NAG-SER         : bond        0.00827 (    6)
  link_NAG-SER         : angle       1.47350 (   12)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.095 
Fit side-chains
REVERT: H   58 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8059 (mtpp)
  outliers start: 10
  outliers final: 10
  residues processed: 42
  average time/residue: 0.0740
  time to fit residues: 3.6969
Evaluate side-chains
  44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   42 SER
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain P residue   37 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain K residue   37 VAL
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   59 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0970
   chunk 22 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    2.0184

-------------------------------------------------------------------------------
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 = 0.4273 r_free = 0.4273 target = 0.133233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.106181 restraints weight = 3597.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 3.25
r_work: 0.3792 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.013   2622  Z= 0.131
  Angle     :  0.430   3.898   3558  Z= 0.232
  Chirality :  0.048   0.117    486
  Planarity :  0.001   0.004    438
  Dihedral  :  3.387  11.212    504
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 0.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 25.21 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.29 (0.41), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.50 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR K  39 
 HIS   0.002   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 2616)
  covalent geometry    : angle       0.42707 ( 3546)
  hydrogen bonds       : bond        0.01037 (   36)
  hydrogen bonds       : angle       3.48005 (  108)
  link_NAG-SER         : bond        0.00544 (    6)
  link_NAG-SER         : angle       1.01907 (   12)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.100 
Fit side-chains
REVERT: H   58 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8058 (mtpp)
  outliers start: 8
  outliers final: 8
  residues processed: 40
  average time/residue: 0.0766
  time to fit residues: 3.6309
Evaluate side-chains
  42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   42 SER
Chi-restraints excluded: chain P residue   37 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain A residue   37 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 13 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 5 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.4303 r_free = 0.4303 target = 0.135246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.108080 restraints weight = 3510.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 3.23
r_work: 0.3821 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   2622  Z= 0.091
  Angle     :  0.390   3.946   3558  Z= 0.211
  Chirality :  0.048   0.119    486
  Planarity :  0.001   0.004    438
  Dihedral  :  3.141  10.259    504
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 26.50 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.12 (0.42), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR P  39 
 HIS   0.002   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 ( 2616)
  covalent geometry    : angle       0.38678 ( 3546)
  hydrogen bonds       : bond        0.00834 (   36)
  hydrogen bonds       : angle       3.41036 (  108)
  link_NAG-SER         : bond        0.00402 (    6)
  link_NAG-SER         : angle       0.89757 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 822.00 seconds
wall clock time: 14 minutes 55.55 seconds (895.55 seconds total)