Starting phenix.real_space_refine
on Fri Aug 22 14:34:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hbw_34645/08_2025/8hbw_34645.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hbw_34645/08_2025/8hbw_34645.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hbw_34645/08_2025/8hbw_34645.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hbw_34645/08_2025/8hbw_34645.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hbw_34645/08_2025/8hbw_34645.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hbw_34645/08_2025/8hbw_34645.map"
  }
  resolution = 2.57
  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=   0.003 sd=   0.159
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       7      5.49       5
     S      18      5.16       5
     C    2109      2.51       5
     N     548      2.21       5
     O     627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3309
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2179
          Classifications: {'peptide': 290}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 15, 'TRANS': 274}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 997
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 997
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "A"
      Number of atoms: 133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 133
          Unusual residues: {'ATP': 1, 'CDL': 1, 'PC1': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 106
          Unresolved non-hydrogen angles: 112
          Unresolved non-hydrogen dihedrals: 102
  Time building chain proxies: 0.94, per 1000 atoms: 0.28
  Number of scatterers: 3309
  At special positions: 0
  Unit cell: (65.052, 71.724, 111.756, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P       7     15.00
     O     627      8.00
     N     548      7.00
     C    2109      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03

  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: 0.29
  Conformation dependent library (CDL) restraints added in 90.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  754

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 3 sheets defined
      62.3% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 42
      Proline residue:  A  32  - end of helix
    Processing helix  chain 'A' and resid 56 through 69
    Processing helix  chain 'A' and resid 70 through 75
    Processing helix  chain 'A' and resid 76 through 94
      removed outlier: 4.367A  pdb=" N   SER A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 104
    Processing helix  chain 'A' and resid 111 through 143
      Proline residue:  A 132  - end of helix
    Processing helix  chain 'A' and resid 155 through 167
    Processing helix  chain 'A' and resid 168 through 174
      removed outlier: 3.629A  pdb=" N   LYS A 174 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 204
    Processing helix  chain 'A' and resid 210 through 242
      removed outlier: 4.224A  pdb=" N   HIS A 214 " --> pdb=" O   ASP A 210 " (cutoff:3.500A)
      Proline residue:  A 231  - end of helix
    Processing helix  chain 'A' and resid 249 through 262
    Processing helix  chain 'A' and resid 263 through 268
    Processing helix  chain 'A' and resid 269 through 298
      removed outlier: 3.609A  pdb=" N   SER A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13
      removed outlier: 6.892A  pdb=" N   VAL B  12 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   MET B  34 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ALA B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13
      removed outlier: 6.892A  pdb=" N   VAL B  12 " --> pdb=" O   SER B 120 " (cutoff:3.500A)

    231 hydrogen bonds defined for protein.
    627 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: 0.56

  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:
        1.20 -     1.32: 547
        1.32 -     1.44: 902
        1.44 -     1.56: 1893
        1.56 -     1.68: 13
        1.68 -     1.81: 27
  Bond restraints: 3382
  Sorted by residual:
  bond pdb=" CA7 CDL A 402 "
       pdb=" OA8 CDL A 402 "
    ideal  model  delta    sigma   weight residual
    1.334  1.454 -0.120 1.10e-02 8.26e+03 1.20e+02
  bond pdb=" CB7 CDL A 402 "
       pdb=" OB8 CDL A 402 "
    ideal  model  delta    sigma   weight residual
    1.334  1.446 -0.112 1.10e-02 8.26e+03 1.03e+02
  bond pdb=" CA5 CDL A 402 "
       pdb=" OA6 CDL A 402 "
    ideal  model  delta    sigma   weight residual
    1.342  1.454 -0.112 1.50e-02 4.44e+03 5.57e+01
  bond pdb=" C4  ATP A 401 "
       pdb=" C5  ATP A 401 "
    ideal  model  delta    sigma   weight residual
    1.388  1.462 -0.074 1.00e-02 1.00e+04 5.43e+01
  bond pdb=" CB5 CDL A 402 "
       pdb=" OB6 CDL A 402 "
    ideal  model  delta    sigma   weight residual
    1.342  1.449 -0.107 1.50e-02 4.44e+03 5.10e+01
  ... (remaining 3377 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.41: 4506
        3.41 -     6.82: 70
        6.82 -    10.22: 14
       10.22 -    13.63: 1
       13.63 -    17.04: 1
  Bond angle restraints: 4592
  Sorted by residual:
  angle pdb=" PB  ATP A 401 "
        pdb=" O3B ATP A 401 "
        pdb=" PG  ATP A 401 "
      ideal   model   delta    sigma   weight residual
     139.87  122.83   17.04 1.00e+00 1.00e+00 2.90e+02
  angle pdb=" PA  ATP A 401 "
        pdb=" O3A ATP A 401 "
        pdb=" PB  ATP A 401 "
      ideal   model   delta    sigma   weight residual
     136.83  124.25   12.58 1.00e+00 1.00e+00 1.58e+02
  angle pdb=" C5  ATP A 401 "
        pdb=" C4  ATP A 401 "
        pdb=" N3  ATP A 401 "
      ideal   model   delta    sigma   weight residual
     126.80  119.46    7.34 1.00e+00 1.00e+00 5.39e+01
  angle pdb=" C11 CDL A 402 "
        pdb=" CA5 CDL A 402 "
        pdb=" OA6 CDL A 402 "
      ideal   model   delta    sigma   weight residual
     111.33  120.23   -8.90 1.32e+00 5.72e-01 4.53e+01
  angle pdb=" N3  ATP A 401 "
        pdb=" C4  ATP A 401 "
        pdb=" N9  ATP A 401 "
      ideal   model   delta    sigma   weight residual
     127.04  134.51   -7.47 1.15e+00 7.59e-01 4.24e+01
  ... (remaining 4587 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 1792
       17.12 -    34.24: 156
       34.24 -    51.36: 64
       51.36 -    68.49: 14
       68.49 -    85.61: 6
  Dihedral angle restraints: 2032
    sinusoidal: 849
      harmonic: 1183
  Sorted by residual:
  dihedral pdb=" CA  ALA A 208 "
           pdb=" C   ALA A 208 "
           pdb=" N   ASP A 209 "
           pdb=" CA  ASP A 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.45  -17.55     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  ASP A 209 "
           pdb=" C   ASP A 209 "
           pdb=" N   ASP A 210 "
           pdb=" CA  ASP A 210 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.97   17.03     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CB  GLU A 100 "
           pdb=" CG  GLU A 100 "
           pdb=" CD  GLU A 100 "
           pdb=" OE1 GLU A 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.61  -85.61     1      3.00e+01 1.11e-03 9.85e+00
  ... (remaining 2029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 331
       0.043 -    0.086: 138
       0.086 -    0.129: 33
       0.129 -    0.172: 5
       0.172 -    0.214: 3
  Chirality restraints: 510
  Sorted by residual:
  chirality pdb=" CA  LYS A  66 "
            pdb=" N   LYS A  66 "
            pdb=" C   LYS A  66 "
            pdb=" CB  LYS A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  GLU A 261 "
            pdb=" N   GLU A 261 "
            pdb=" C   GLU A 261 "
            pdb=" CB  GLU A 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.07e-01
  chirality pdb=" CA  ARG A 238 "
            pdb=" N   ARG A 238 "
            pdb=" C   ARG A 238 "
            pdb=" CB  ARG A 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.49e-01
  ... (remaining 507 not shown)

  Planarity restraints: 567
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A   9 "   -0.038 5.00e-02 4.00e+02   5.71e-02 5.22e+00
        pdb=" N   PRO A  10 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  10 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  10 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  84 "    0.011 2.00e-02 2.50e+03   2.23e-02 4.96e+00
        pdb=" C   GLN A  84 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   GLN A  84 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ILE A  85 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 101 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   PHE B 101 "    0.030 2.00e-02 2.50e+03
        pdb=" O   PHE B 101 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLY B 102 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 564 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 360
        2.74 -     3.28: 3189
        3.28 -     3.82: 5979
        3.82 -     4.36: 7174
        4.36 -     4.90: 12102
  Nonbonded interactions: 28804
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 103 "
            pdb=" O   THR A 108 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OE2 GLU A  45 "
            pdb=" OH  TYR A 247 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   LYS A 292 "
            pdb=" OG  SER A 296 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   GLY A 130 "
            pdb=" OG1 THR A 133 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   TRP A 173 "
            pdb=" OG1 THR A 176 "
     model   vdw
     2.323 3.040
  ... (remaining 28799 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.680
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.110
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
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      :  0.010   0.124   3383  Z= 0.619
  Angle     :  1.055  17.042   4594  Z= 0.645
  Chirality :  0.050   0.214    510
  Planarity :  0.005   0.057    567
  Dihedral  : 16.265  85.607   1275
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.39), residues: 410
  helix:  1.83 (0.32), residues: 221
  sheet: -0.32 (0.61), residues: 60
  loop :  0.59 (0.54), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG B 104 
 TYR   0.014   0.002   TYR A 157 
 PHE   0.018   0.003   PHE A 223 
 TRP   0.007   0.002   TRP A 173 
 HIS   0.003   0.001   HIS B 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.01032 ( 3382)
  covalent geometry    : angle       1.05315 ( 4592)
  SS BOND              : bond        0.00499 (    1)
  SS BOND              : angle       3.02118 (    2)
  hydrogen bonds       : bond        0.10650 (  227)
  hydrogen bonds       : angle       6.85175 (  627)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.8108 (tttp) cc_final: 0.7810 (tptp)
REVERT: A  161 ARG cc_start: 0.7447 (ttt180) cc_final: 0.6715 (mtt90)
REVERT: A  206 ILE cc_start: 0.6885 (mm) cc_final: 0.6564 (mp)
REVERT: A  248 LYS cc_start: 0.8664 (ptmm) cc_final: 0.8426 (ptmt)
REVERT: A  293 ARG cc_start: 0.6520 (ptm-80) cc_final: 0.6132 (tmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.6899
  time to fit residues: 43.7085
Evaluate side-chains
  53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.134810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.120409 restraints weight = 3591.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 0.90
r_work: 0.3221 rms_B_bonded: 1.25 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 2.20 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   3383  Z= 0.140
  Angle     :  0.533   6.793   4594  Z= 0.282
  Chirality :  0.040   0.139    510
  Planarity :  0.005   0.051    567
  Dihedral  : 13.655  78.796    569
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  9.20 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.40), residues: 410
  helix:  2.68 (0.32), residues: 221
  sheet:  0.06 (0.65), residues: 54
  loop :  0.66 (0.54), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  72 
 TYR   0.007   0.001   TYR A  74 
 PHE   0.009   0.001   PHE A 223 
 TRP   0.008   0.001   TRP B 111 
 HIS   0.002   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3382)
  covalent geometry    : angle       0.53253 ( 4592)
  SS BOND              : bond        0.00206 (    1)
  SS BOND              : angle       1.53732 (    2)
  hydrogen bonds       : bond        0.03849 (  227)
  hydrogen bonds       : angle       5.55785 (  627)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.8320 (tttp) cc_final: 0.7842 (tptp)
REVERT: A  117 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7634 (tt)
REVERT: A  161 ARG cc_start: 0.7963 (ttt180) cc_final: 0.6647 (mtt90)
REVERT: A  206 ILE cc_start: 0.6778 (mm) cc_final: 0.6411 (mp)
REVERT: A  293 ARG cc_start: 0.6391 (ptm-80) cc_final: 0.6012 (tmt-80)
  outliers start: 5
  outliers final: 0
  residues processed: 64
  average time/residue: 0.5893
  time to fit residues: 38.6849
Evaluate side-chains
  56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.133812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.119258 restraints weight = 3602.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 0.91
r_work: 0.3197 rms_B_bonded: 1.29 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 2.29 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3383  Z= 0.155
  Angle     :  0.539   7.363   4594  Z= 0.281
  Chirality :  0.041   0.140    510
  Planarity :  0.005   0.047    567
  Dihedral  : 12.796  72.185    569
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 11.28 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.40), residues: 410
  helix:  2.94 (0.32), residues: 221
  sheet:  0.01 (0.65), residues: 54
  loop :  0.61 (0.53), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  72 
 TYR   0.010   0.001   TYR A 157 
 PHE   0.012   0.002   PHE A 223 
 TRP   0.005   0.001   TRP A 280 
 HIS   0.002   0.001   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 3382)
  covalent geometry    : angle       0.53831 ( 4592)
  SS BOND              : bond        0.00274 (    1)
  SS BOND              : angle       1.60028 (    2)
  hydrogen bonds       : bond        0.03879 (  227)
  hydrogen bonds       : angle       5.53904 (  627)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.8344 (tttp) cc_final: 0.7852 (tptp)
REVERT: A   57 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8173 (t)
REVERT: A  117 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7662 (tt)
REVERT: A  161 ARG cc_start: 0.7993 (ttt180) cc_final: 0.6667 (mtt90)
REVERT: A  206 ILE cc_start: 0.6792 (mm) cc_final: 0.6439 (mp)
REVERT: A  293 ARG cc_start: 0.6469 (ptm-80) cc_final: 0.6100 (tmt-80)
  outliers start: 9
  outliers final: 5
  residues processed: 60
  average time/residue: 0.6606
  time to fit residues: 40.6344
Evaluate side-chains
  59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain B residue   53 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 28 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.134481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.119494 restraints weight = 3620.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 0.95
r_work: 0.3209 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 2.40 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   3383  Z= 0.139
  Angle     :  0.526   7.967   4594  Z= 0.272
  Chirality :  0.040   0.135    510
  Planarity :  0.005   0.043    567
  Dihedral  : 12.378  71.731    569
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 12.17 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.78 (0.40), residues: 410
  helix:  3.00 (0.32), residues: 221
  sheet:  0.11 (0.66), residues: 54
  loop :  0.69 (0.53), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  72 
 TYR   0.008   0.001   TYR A 157 
 PHE   0.010   0.001   PHE A 223 
 TRP   0.005   0.001   TRP A 280 
 HIS   0.001   0.000   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3382)
  covalent geometry    : angle       0.52582 ( 4592)
  SS BOND              : bond        0.00181 (    1)
  SS BOND              : angle       1.37866 (    2)
  hydrogen bonds       : bond        0.03673 (  227)
  hydrogen bonds       : angle       5.41117 (  627)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7403 (tpt-90)
REVERT: A   55 LYS cc_start: 0.8329 (tttp) cc_final: 0.7823 (tptp)
REVERT: A   57 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8172 (t)
REVERT: A   70 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6502 (mtp-110)
REVERT: A  117 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7616 (tt)
REVERT: A  161 ARG cc_start: 0.8009 (ttt180) cc_final: 0.6618 (mtt90)
REVERT: A  206 ILE cc_start: 0.6635 (mm) cc_final: 0.6302 (mp)
REVERT: A  293 ARG cc_start: 0.6474 (ptm-80) cc_final: 0.6105 (tmt-80)
  outliers start: 10
  outliers final: 4
  residues processed: 58
  average time/residue: 0.6429
  time to fit residues: 38.2240
Evaluate side-chains
  62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain B residue   53 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0670
   chunk 21 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.135219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.120219 restraints weight = 3580.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 0.95
r_work: 0.3220 rms_B_bonded: 1.37 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 2.40 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3383  Z= 0.131
  Angle     :  0.516   8.335   4594  Z= 0.265
  Chirality :  0.040   0.129    510
  Planarity :  0.004   0.041    567
  Dihedral  : 12.009  70.854    569
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 13.06 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.90 (0.40), residues: 410
  helix:  3.10 (0.32), residues: 221
  sheet:  0.16 (0.66), residues: 54
  loop :  0.74 (0.53), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  72 
 TYR   0.008   0.001   TYR A 157 
 PHE   0.009   0.001   PHE A 223 
 TRP   0.006   0.001   TRP A 280 
 HIS   0.001   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3382)
  covalent geometry    : angle       0.51532 ( 4592)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       1.27745 (    2)
  hydrogen bonds       : bond        0.03565 (  227)
  hydrogen bonds       : angle       5.29698 (  627)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7452 (tpt-90)
REVERT: A   55 LYS cc_start: 0.8314 (tttp) cc_final: 0.7820 (tptp)
REVERT: A   57 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8155 (t)
REVERT: A   70 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6522 (mtp-110)
REVERT: A  117 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7619 (tt)
REVERT: A  161 ARG cc_start: 0.8009 (ttt180) cc_final: 0.6624 (mtt90)
REVERT: A  206 ILE cc_start: 0.6469 (mm) cc_final: 0.6144 (mp)
REVERT: A  293 ARG cc_start: 0.6451 (ptm-80) cc_final: 0.6092 (tmt-80)
  outliers start: 10
  outliers final: 4
  residues processed: 63
  average time/residue: 0.5171
  time to fit residues: 33.4761
Evaluate side-chains
  62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain B residue   53 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 187 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.132900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.118712 restraints weight = 3578.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 0.87
r_work: 0.3193 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 2.18 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   3383  Z= 0.181
  Angle     :  0.565   8.061   4594  Z= 0.292
  Chirality :  0.042   0.127    510
  Planarity :  0.005   0.039    567
  Dihedral  : 12.570  72.810    569
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.54 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.73 (0.40), residues: 410
  helix:  2.93 (0.32), residues: 222
  sheet: -0.06 (0.65), residues: 54
  loop :  0.76 (0.53), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  72 
 TYR   0.010   0.001   TYR A 157 
 PHE   0.014   0.002   PHE A 223 
 TRP   0.004   0.001   TRP B  57 
 HIS   0.002   0.001   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 3382)
  covalent geometry    : angle       0.56364 ( 4592)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       1.75771 (    2)
  hydrogen bonds       : bond        0.03994 (  227)
  hydrogen bonds       : angle       5.49940 (  627)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7270 (tpt-90)
REVERT: A   55 LYS cc_start: 0.8365 (tttp) cc_final: 0.7862 (tptp)
REVERT: A   57 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8192 (t)
REVERT: A   70 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6570 (mtp-110)
REVERT: A  117 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7659 (tt)
REVERT: A  161 ARG cc_start: 0.8017 (ttt180) cc_final: 0.6641 (mtt90)
REVERT: A  206 ILE cc_start: 0.6781 (mm) cc_final: 0.6435 (mp)
REVERT: A  293 ARG cc_start: 0.6468 (ptm-80) cc_final: 0.6069 (tmt-80)
  outliers start: 10
  outliers final: 5
  residues processed: 58
  average time/residue: 0.5823
  time to fit residues: 34.6914
Evaluate side-chains
  63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain B residue   53 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 38 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9980
   chunk 1 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 187 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.134528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.119426 restraints weight = 3632.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 0.95
r_work: 0.3217 rms_B_bonded: 1.36 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   3383  Z= 0.134
  Angle     :  0.527   8.588   4594  Z= 0.270
  Chirality :  0.040   0.128    510
  Planarity :  0.004   0.038    567
  Dihedral  : 12.167  71.864    569
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.24 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.87 (0.40), residues: 410
  helix:  3.03 (0.32), residues: 222
  sheet:  0.12 (0.66), residues: 54
  loop :  0.80 (0.52), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  72 
 TYR   0.008   0.001   TYR A 157 
 PHE   0.012   0.002   PHE B 101 
 TRP   0.006   0.001   TRP A 280 
 HIS   0.001   0.000   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3382)
  covalent geometry    : angle       0.52633 ( 4592)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       1.23219 (    2)
  hydrogen bonds       : bond        0.03640 (  227)
  hydrogen bonds       : angle       5.30163 (  627)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7473 (tpt-90)
REVERT: A   55 LYS cc_start: 0.8355 (tttp) cc_final: 0.7855 (tptp)
REVERT: A   57 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8159 (t)
REVERT: A   70 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6585 (mtp-110)
REVERT: A  117 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7614 (tt)
REVERT: A  161 ARG cc_start: 0.8018 (ttt180) cc_final: 0.6637 (mtt90)
REVERT: A  206 ILE cc_start: 0.6526 (mm) cc_final: 0.6193 (mp)
REVERT: A  293 ARG cc_start: 0.6478 (ptm-80) cc_final: 0.6095 (tmt-80)
  outliers start: 10
  outliers final: 5
  residues processed: 63
  average time/residue: 0.5962
  time to fit residues: 38.4885
Evaluate side-chains
  65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain B residue   53 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0270
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 187 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.134929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.119904 restraints weight = 3643.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 0.95
r_work: 0.3214 rms_B_bonded: 1.36 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   3383  Z= 0.135
  Angle     :  0.531   8.573   4594  Z= 0.274
  Chirality :  0.039   0.123    510
  Planarity :  0.005   0.038    567
  Dihedral  : 12.012  71.488    569
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.84 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.89 (0.40), residues: 410
  helix:  3.06 (0.32), residues: 222
  sheet:  0.16 (0.67), residues: 54
  loop :  0.78 (0.52), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 104 
 TYR   0.008   0.001   TYR A 157 
 PHE   0.011   0.002   PHE B 101 
 TRP   0.006   0.001   TRP B 105 
 HIS   0.001   0.001   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3382)
  covalent geometry    : angle       0.53094 ( 4592)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       1.24031 (    2)
  hydrogen bonds       : bond        0.03610 (  227)
  hydrogen bonds       : angle       5.25513 (  627)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7486 (tpt-90)
REVERT: A   55 LYS cc_start: 0.8356 (tttp) cc_final: 0.7853 (tptp)
REVERT: A   57 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8156 (t)
REVERT: A   70 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6559 (mtp-110)
REVERT: A  117 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7605 (tt)
REVERT: A  161 ARG cc_start: 0.8010 (ttt180) cc_final: 0.6617 (mtt90)
REVERT: A  206 ILE cc_start: 0.6488 (mm) cc_final: 0.6155 (mp)
REVERT: A  293 ARG cc_start: 0.6426 (ptm-80) cc_final: 0.6072 (tmt-80)
  outliers start: 10
  outliers final: 5
  residues processed: 61
  average time/residue: 0.5990
  time to fit residues: 37.5022
Evaluate side-chains
  64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain B residue   53 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 187 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.136074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.120332 restraints weight = 3756.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.06
r_work: 0.3237 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3383  Z= 0.156
  Angle     :  0.551   8.557   4594  Z= 0.285
  Chirality :  0.041   0.126    510
  Planarity :  0.005   0.037    567
  Dihedral  : 12.135  71.643    569
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.73 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.81 (0.40), residues: 410
  helix:  3.00 (0.32), residues: 222
  sheet:  0.11 (0.67), residues: 54
  loop :  0.75 (0.52), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  72 
 TYR   0.009   0.001   TYR A 157 
 PHE   0.012   0.002   PHE A 223 
 TRP   0.007   0.001   TRP B 105 
 HIS   0.002   0.001   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 3382)
  covalent geometry    : angle       0.55048 ( 4592)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       1.48090 (    2)
  hydrogen bonds       : bond        0.03810 (  227)
  hydrogen bonds       : angle       5.33106 (  627)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7294 (tpt-90)
REVERT: A   55 LYS cc_start: 0.8413 (tttp) cc_final: 0.7923 (tptp)
REVERT: A   57 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8155 (t)
REVERT: A   70 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6679 (mtp-110)
REVERT: A  117 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7691 (tt)
REVERT: A  161 ARG cc_start: 0.8059 (ttt180) cc_final: 0.6698 (mtt90)
REVERT: A  206 ILE cc_start: 0.6628 (mm) cc_final: 0.6287 (mp)
REVERT: A  293 ARG cc_start: 0.6484 (ptm-80) cc_final: 0.6114 (tmt-80)
  outliers start: 9
  outliers final: 5
  residues processed: 57
  average time/residue: 0.6278
  time to fit residues: 36.7305
Evaluate side-chains
  63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain B residue   53 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0980
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0470
   chunk 34 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 187 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.138416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.122693 restraints weight = 3733.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.07
r_work: 0.3264 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3383  Z= 0.120
  Angle     :  0.521   8.946   4594  Z= 0.267
  Chirality :  0.039   0.127    510
  Planarity :  0.004   0.037    567
  Dihedral  : 11.761  71.109    569
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.73 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.98 (0.40), residues: 410
  helix:  3.13 (0.32), residues: 222
  sheet:  0.31 (0.69), residues: 54
  loop :  0.76 (0.52), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 238 
 TYR   0.007   0.001   TYR A 157 
 PHE   0.008   0.001   PHE B 101 
 TRP   0.007   0.001   TRP A 280 
 HIS   0.001   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3382)
  covalent geometry    : angle       0.52082 ( 4592)
  SS BOND              : bond        0.00077 (    1)
  SS BOND              : angle       1.03272 (    2)
  hydrogen bonds       : bond        0.03509 (  227)
  hydrogen bonds       : angle       5.17083 (  627)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7510 (tmt170)
REVERT: A   55 LYS cc_start: 0.8380 (tttp) cc_final: 0.7877 (tptp)
REVERT: A   57 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8128 (t)
REVERT: A   70 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6647 (mtp-110)
REVERT: A  117 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7671 (tt)
REVERT: A  161 ARG cc_start: 0.8044 (ttt180) cc_final: 0.6670 (mtt90)
REVERT: A  206 ILE cc_start: 0.6489 (mm) cc_final: 0.6163 (mp)
REVERT: A  293 ARG cc_start: 0.6473 (ptm-80) cc_final: 0.6114 (tmt-80)
  outliers start: 9
  outliers final: 4
  residues processed: 60
  average time/residue: 0.6079
  time to fit residues: 37.3884
Evaluate side-chains
  62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain B residue   53 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0970
   chunk 11 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 9 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 187 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.135732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.119874 restraints weight = 3716.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.10
r_work: 0.3203 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3383  Z= 0.131
  Angle     :  0.529   8.154   4594  Z= 0.271
  Chirality :  0.039   0.122    510
  Planarity :  0.005   0.037    567
  Dihedral  : 11.703  70.968    569
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.73 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.96 (0.40), residues: 410
  helix:  3.10 (0.32), residues: 222
  sheet:  0.30 (0.68), residues: 54
  loop :  0.79 (0.52), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 238 
 TYR   0.008   0.001   TYR A 157 
 PHE   0.010   0.002   PHE A 285 
 TRP   0.006   0.001   TRP B 103 
 HIS   0.001   0.000   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3382)
  covalent geometry    : angle       0.52838 ( 4592)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       1.49824 (    2)
  hydrogen bonds       : bond        0.03584 (  227)
  hydrogen bonds       : angle       5.17233 (  627)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1484.14 seconds
wall clock time: 25 minutes 59.39 seconds (1559.39 seconds total)