Starting phenix.real_space_refine
on Wed Sep 17 05:49:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w2s_43757/09_2025/8w2s_43757.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w2s_43757/09_2025/8w2s_43757.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w2s_43757/09_2025/8w2s_43757.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w2s_43757/09_2025/8w2s_43757.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w2s_43757/09_2025/8w2s_43757.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w2s_43757/09_2025/8w2s_43757.cif"
  }
  resolution = 3.4
  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=   0.047
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     137      5.49       5
     S      11      5.16       5
     C    3025      2.51       5
     N    1051      2.21       5
     O    1464      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: 5688
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2761
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 6, 'TRANS': 332}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 97
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 43
    Chain: "B"
      Number of atoms: 2927
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 2927
          Classifications: {'RNA': 137}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 69, 'rna3p_pyr': 55}
          Link IDs: {'rna2p': 13, 'rna3p': 123}
  Time building chain proxies: 1.56, per 1000 atoms: 0.27
  Number of scatterers: 5688
  At special positions: 0
  Unit cell: (86.6528, 86.6528, 115.815, 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      11     16.00
     P     137     15.00
     O    1464      8.00
     N    1051      7.00
     C    3025      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 132.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  652

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 2 sheets defined
      56.0% alpha, 5.3% beta
      50 base pairs and 94 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 75
      removed outlier: 3.690A  pdb=" N   GLY A  75 " --> pdb=" O   LEU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 91
      removed outlier: 3.836A  pdb=" N   GLU A  84 " --> pdb=" O   THR A  80 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   HIS A  91 " --> pdb=" O   TYR A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 99
    Processing helix  chain 'A' and resid 105 through 110
    Processing helix  chain 'A' and resid 113 through 132
      removed outlier: 3.665A  pdb=" N   ARG A 132 " --> pdb=" O   GLU A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 151
    Processing helix  chain 'A' and resid 154 through 167
    Processing helix  chain 'A' and resid 197 through 207
    Processing helix  chain 'A' and resid 212 through 225
      removed outlier: 3.521A  pdb=" N   ASP A 225 " --> pdb=" O   ASP A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 239
    Processing helix  chain 'A' and resid 242 through 254
      removed outlier: 3.518A  pdb=" N   ARG A 246 " --> pdb=" O   ASP A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 268
      removed outlier: 3.617A  pdb=" N   ILE A 268 " --> pdb=" O   LYS A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 583
      removed outlier: 4.166A  pdb=" N   GLU A 580 " --> pdb=" O   CYS A 577 " (cutoff:3.500A)
      removed outlier: 5.398A  pdb=" N   ASP A 581 " --> pdb=" O   GLY A 578 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A 583 " --> pdb=" O   GLU A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 599
    Processing helix  chain 'A' and resid 608 through 614
    Processing sheet with id=AA1, first strand: chain 'A' and resid 560 through 562
    Processing sheet with id=AA2, first strand: chain 'A' and resid 640 through 643
      removed outlier: 3.569A  pdb=" N   ILE A 641 " --> pdb=" O   PHE A 648 " (cutoff:3.500A)

    134 hydrogen bonds defined for protein.
    378 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      120 hydrogen bonds
      200 hydrogen bond angles
      0 basepair planarities
      50 basepair parallelities
      94 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1109
        1.33 -     1.45: 2107
        1.45 -     1.57: 2567
        1.57 -     1.69: 273
        1.69 -     1.81: 16
  Bond restraints: 6072
  Sorted by residual:
  bond pdb=" CB  GLU A 107 "
       pdb=" CG  GLU A 107 "
    ideal  model  delta    sigma   weight residual
    1.520  1.568 -0.048 3.00e-02 1.11e+03 2.58e+00
  bond pdb=" C3'   U B  92 "
       pdb=" O3'   U B  92 "
    ideal  model  delta    sigma   weight residual
    1.427  1.451 -0.024 1.50e-02 4.44e+03 2.51e+00
  bond pdb=" CG1 ILE A 252 "
       pdb=" CD1 ILE A 252 "
    ideal  model  delta    sigma   weight residual
    1.513  1.454  0.059 3.90e-02 6.57e+02 2.31e+00
  bond pdb=" CB  LYS A 124 "
       pdb=" CG  LYS A 124 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.94e+00
  bond pdb=" O3'   G B 142 "
       pdb=" P     G B 143 "
    ideal  model  delta    sigma   weight residual
    1.607  1.627 -0.020 1.50e-02 4.44e+03 1.82e+00
  ... (remaining 6067 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.69: 8670
        2.69 -     5.37: 130
        5.37 -     8.06: 27
        8.06 -    10.74: 6
       10.74 -    13.43: 4
  Bond angle restraints: 8837
  Sorted by residual:
  angle pdb=" N   LYS A 172 "
        pdb=" CA  LYS A 172 "
        pdb=" C   LYS A 172 "
      ideal   model   delta    sigma   weight residual
     108.67   95.45   13.22 1.55e+00 4.16e-01 7.27e+01
  angle pdb=" N   ARG A 198 "
        pdb=" CA  ARG A 198 "
        pdb=" C   ARG A 198 "
      ideal   model   delta    sigma   weight residual
     111.33  120.20   -8.87 1.21e+00 6.83e-01 5.38e+01
  angle pdb=" C2'   G B 142 "
        pdb=" C1'   G B 142 "
        pdb=" N9    G B 142 "
      ideal   model   delta    sigma   weight residual
     114.00  124.83  -10.83 1.50e+00 4.44e-01 5.21e+01
  angle pdb=" O4'   G B 142 "
        pdb=" C1'   G B 142 "
        pdb=" N9    G B 142 "
      ideal   model   delta    sigma   weight residual
     108.20  117.21   -9.01 1.50e+00 4.44e-01 3.61e+01
  angle pdb=" N   THR A 261 "
        pdb=" CA  THR A 261 "
        pdb=" C   THR A 261 "
      ideal   model   delta    sigma   weight residual
     108.63   99.71    8.92 1.60e+00 3.91e-01 3.10e+01
  ... (remaining 8832 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.33: 3552
       35.33 -    70.66: 282
       70.66 -   105.99: 33
      105.99 -   141.32: 1
      141.32 -   176.65: 2
  Dihedral angle restraints: 3870
    sinusoidal: 2874
      harmonic: 996
  Sorted by residual:
  dihedral pdb=" O4'   U B  92 "
           pdb=" C1'   U B  92 "
           pdb=" N1    U B  92 "
           pdb=" C2    U B  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   48.65 -176.65     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" CA  LYS A 181 "
           pdb=" C   LYS A 181 "
           pdb=" N   CYS A 182 "
           pdb=" CA  CYS A 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.49   26.51     0      5.00e+00 4.00e-02 2.81e+01
  dihedral pdb=" O4'   G B 142 "
           pdb=" C1'   G B 142 "
           pdb=" N9    G B 142 "
           pdb=" C4    G B 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
     254.00  176.43   77.57     1      1.70e+01 3.46e-03 2.61e+01
  ... (remaining 3867 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.175: 1085
       0.175 -    0.350: 3
       0.350 -    0.524: 0
       0.524 -    0.699: 0
       0.699 -    0.874: 1
  Chirality restraints: 1089
  Sorted by residual:
  chirality pdb=" C1'   G B 142 "
            pdb=" O4'   G B 142 "
            pdb=" C2'   G B 142 "
            pdb=" N9    G B 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.56    0.87 2.00e-01 2.50e+01 1.91e+01
  chirality pdb=" C3'   U B  92 "
            pdb=" C4'   U B  92 "
            pdb=" O3'   U B  92 "
            pdb=" C2'   U B  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.47   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" C3'   G B 122 "
            pdb=" C4'   G B 122 "
            pdb=" O3'   G B 122 "
            pdb=" C2'   G B 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.20   -0.28 2.00e-01 2.50e+01 1.92e+00
  ... (remaining 1086 not shown)

  Planarity restraints: 621
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 142 "    0.066 2.00e-02 2.50e+03   3.07e-02 2.82e+01
        pdb=" N9    G B 142 "   -0.081 2.00e-02 2.50e+03
        pdb=" C8    G B 142 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G B 142 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B 142 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    G B 142 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G B 142 "    0.020 2.00e-02 2.50e+03
        pdb=" N1    G B 142 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    G B 142 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2    G B 142 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G B 142 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4    G B 142 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 137 "   -0.010 2.00e-02 2.50e+03   2.03e-02 4.14e+00
        pdb=" C   ARG A 137 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ARG A 137 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS A 138 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 173 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.88e+00
        pdb=" C   ARG A 173 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ARG A 173 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   PHE A 174 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 618 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1441
        2.81 -     3.33: 5025
        3.33 -     3.86: 11190
        3.86 -     4.38: 12754
        4.38 -     4.90: 17411
  Nonbonded interactions: 47821
  Sorted by model distance:
  nonbonded pdb=" O2'   G B  11 "
            pdb=" O4'   A B  12 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OP2   U B  91 "
            pdb=" O2'   U B  92 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   PRO A 558 "
            pdb=" O2'   U B  22 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OE1 GLU A 212 "
            pdb=" OG  SER A 214 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" N2    G B 117 "
            pdb=" OP2   A B 120 "
     model   vdw
     2.340 3.120
  ... (remaining 47816 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:             2.570
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.310
  Find NCS groups from input model:        0.020
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
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      :  0.004   0.059   6072  Z= 0.193
  Angle     :  0.889  13.428   8837  Z= 0.484
  Chirality :  0.049   0.874   1089
  Planarity :  0.005   0.048    621
  Dihedral  : 20.847 176.648   3218
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.33 %
    Favored  : 85.67 %
  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: -1.36 (0.44), residues: 331
  helix: -0.51 (0.37), residues: 170
  sheet:  1.34 (1.12), residues: 10
  loop : -1.46 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 173 
 TYR   0.021   0.003   TYR A  97 
 PHE   0.016   0.002   PHE A 236 
 TRP   0.013   0.002   TRP A 127 
 HIS   0.008   0.002   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6072)
  covalent geometry    : angle       0.88934 ( 8837)
  hydrogen bonds       : bond        0.12798 (  254)
  hydrogen bonds       : angle       5.40498 (  578)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8091 (tppt) cc_final: 0.7772 (mtpt)
REVERT: A  248 GLN cc_start: 0.9077 (mt0) cc_final: 0.8659 (mp10)
REVERT: A  579 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7958 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1172
  time to fit residues: 7.4587
Evaluate side-chains
  49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.150178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.106224 restraints weight = 11898.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.08
r_work: 0.3419 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6072  Z= 0.148
  Angle     :  0.596   9.627   8837  Z= 0.325
  Chirality :  0.040   0.660   1089
  Planarity :  0.004   0.031    621
  Dihedral  : 21.695 165.877   2488
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 11.95 %
    Favored  : 84.98 %
  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: -0.19 (0.48), residues: 331
  helix:  0.68 (0.40), residues: 174
  sheet:  1.07 (1.18), residues: 10
  loop : -1.19 (0.55), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 173 
 TYR   0.014   0.002   TYR A  97 
 PHE   0.011   0.001   PHE A 570 
 TRP   0.009   0.001   TRP A 120 
 HIS   0.002   0.001   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6072)
  covalent geometry    : angle       0.59617 ( 8837)
  hydrogen bonds       : bond        0.04711 (  254)
  hydrogen bonds       : angle       3.72434 (  578)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 GLN cc_start: 0.9044 (mt0) cc_final: 0.8566 (mp10)
REVERT: A  579 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8169 (mtpp)
  outliers start: 9
  outliers final: 5
  residues processed: 56
  average time/residue: 0.1203
  time to fit residues: 8.2037
Evaluate side-chains
  52 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  619 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:   20.0000
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    0.4980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 645 ASN
A 646 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.145062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.100655 restraints weight = 11648.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.07
r_work: 0.3320 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6072  Z= 0.155
  Angle     :  0.579   9.512   8837  Z= 0.314
  Chirality :  0.040   0.648   1089
  Planarity :  0.004   0.034    621
  Dihedral  : 21.563 167.333   2488
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 12.63 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.40 (0.49), residues: 331
  helix:  1.29 (0.41), residues: 174
  sheet:  1.08 (1.17), residues: 10
  loop : -1.06 (0.57), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 137 
 TYR   0.014   0.002   TYR A  76 
 PHE   0.010   0.002   PHE A 570 
 TRP   0.007   0.001   TRP A 120 
 HIS   0.003   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6072)
  covalent geometry    : angle       0.57931 ( 8837)
  hydrogen bonds       : bond        0.04740 (  254)
  hydrogen bonds       : angle       3.55425 (  578)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 ARG cc_start: 0.8975 (mmm160) cc_final: 0.8739 (mmm160)
REVERT: A  248 GLN cc_start: 0.9019 (mt0) cc_final: 0.8524 (mp10)
REVERT: A  579 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8190 (mtpp)
  outliers start: 11
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1193
  time to fit residues: 8.1652
Evaluate side-chains
  49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  619 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 19 optimal weight:    0.3980
   chunk 36 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0010
   chunk 44 optimal weight:    9.9990
   overall best weight:    1.2390

-------------------------------------------------------------------------------
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 = 0.4133 r_free = 0.4133 target = 0.142542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.097931 restraints weight = 11648.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.12
r_work: 0.3286 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6072  Z= 0.180
  Angle     :  0.589   9.631   8837  Z= 0.319
  Chirality :  0.041   0.661   1089
  Planarity :  0.004   0.034    621
  Dihedral  : 21.474 166.214   2488
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 12.63 %
    Favored  : 82.94 %
  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:  0.53 (0.49), residues: 331
  helix:  1.45 (0.40), residues: 174
  sheet:  1.10 (1.14), residues: 10
  loop : -1.08 (0.58), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 152 
 TYR   0.015   0.002   TYR A  76 
 PHE   0.024   0.002   PHE A 236 
 TRP   0.008   0.001   TRP A 120 
 HIS   0.004   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6072)
  covalent geometry    : angle       0.58924 ( 8837)
  hydrogen bonds       : bond        0.05113 (  254)
  hydrogen bonds       : angle       3.52752 (  578)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 GLN cc_start: 0.8992 (mt0) cc_final: 0.8475 (mp10)
REVERT: A  579 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8212 (mtpp)
REVERT: A  607 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.5196 (tt)
REVERT: A  611 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8123 (tp30)
  outliers start: 13
  outliers final: 6
  residues processed: 57
  average time/residue: 0.1257
  time to fit residues: 8.6645
Evaluate side-chains
  54 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   95 TYR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  611 GLU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  649 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.142808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.098522 restraints weight = 11821.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.12
r_work: 0.3301 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6072  Z= 0.156
  Angle     :  0.565   9.366   8837  Z= 0.305
  Chirality :  0.039   0.635   1089
  Planarity :  0.003   0.033    621
  Dihedral  : 21.384 165.092   2488
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 12.63 %
    Favored  : 84.30 %
  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:  0.67 (0.49), residues: 331
  helix:  1.68 (0.41), residues: 174
  sheet:  0.92 (1.10), residues: 10
  loop : -1.14 (0.57), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 152 
 TYR   0.014   0.002   TYR A  76 
 PHE   0.008   0.001   PHE A  83 
 TRP   0.008   0.001   TRP A 120 
 HIS   0.003   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6072)
  covalent geometry    : angle       0.56549 ( 8837)
  hydrogen bonds       : bond        0.04584 (  254)
  hydrogen bonds       : angle       3.40561 (  578)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 GLN cc_start: 0.9052 (mt0) cc_final: 0.8531 (mp10)
REVERT: A  579 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8222 (mtpp)
REVERT: A  607 LEU cc_start: 0.5584 (OUTLIER) cc_final: 0.5229 (tt)
REVERT: A  649 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7908 (tmmt)
  outliers start: 9
  outliers final: 5
  residues processed: 53
  average time/residue: 0.1307
  time to fit residues: 8.4474
Evaluate side-chains
  52 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  649 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 35 optimal weight:    8.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.145062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.101171 restraints weight = 11753.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 2.10
r_work: 0.3353 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6072  Z= 0.138
  Angle     :  0.555   9.288   8837  Z= 0.300
  Chirality :  0.039   0.619   1089
  Planarity :  0.003   0.034    621
  Dihedral  : 21.347 164.585   2488
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 12.97 %
    Favored  : 83.96 %
  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:  0.66 (0.49), residues: 331
  helix:  1.76 (0.40), residues: 174
  sheet:  0.90 (1.11), residues: 10
  loop : -1.28 (0.56), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 228 
 TYR   0.011   0.002   TYR A  76 
 PHE   0.008   0.001   PHE A 236 
 TRP   0.006   0.001   TRP A 120 
 HIS   0.002   0.000   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6072)
  covalent geometry    : angle       0.55525 ( 8837)
  hydrogen bonds       : bond        0.04407 (  254)
  hydrogen bonds       : angle       3.36595 (  578)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 ARG cc_start: 0.8788 (mmm160) cc_final: 0.8463 (mmm160)
REVERT: A  248 GLN cc_start: 0.9051 (mt0) cc_final: 0.8541 (mp10)
REVERT: A  579 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8168 (mtpp)
REVERT: A  607 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.5036 (tt)
  outliers start: 9
  outliers final: 5
  residues processed: 52
  average time/residue: 0.1208
  time to fit residues: 7.6325
Evaluate side-chains
  50 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  649 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.142224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.097927 restraints weight = 11894.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.16
r_work: 0.3303 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6072  Z= 0.177
  Angle     :  0.586   9.604   8837  Z= 0.316
  Chirality :  0.040   0.665   1089
  Planarity :  0.004   0.035    621
  Dihedral  : 21.345 164.824   2488
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 13.31 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.66 (0.49), residues: 331
  helix:  1.80 (0.40), residues: 174
  sheet:  1.09 (1.11), residues: 10
  loop : -1.36 (0.56), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 152 
 TYR   0.011   0.002   TYR A  76 
 PHE   0.012   0.001   PHE A  83 
 TRP   0.008   0.002   TRP A 120 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6072)
  covalent geometry    : angle       0.58551 ( 8837)
  hydrogen bonds       : bond        0.05138 (  254)
  hydrogen bonds       : angle       3.45406 (  578)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 GLN cc_start: 0.9046 (mt0) cc_final: 0.8528 (mp10)
REVERT: A  579 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8227 (mtpp)
REVERT: A  607 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.4971 (tt)
  outliers start: 9
  outliers final: 6
  residues processed: 52
  average time/residue: 0.1104
  time to fit residues: 7.0796
Evaluate side-chains
  50 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  649 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    0.3980
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.4130 r_free = 0.4130 target = 0.142074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.098516 restraints weight = 11853.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.14
r_work: 0.3310 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6072  Z= 0.174
  Angle     :  0.580   9.474   8837  Z= 0.312
  Chirality :  0.040   0.648   1089
  Planarity :  0.004   0.035    621
  Dihedral  : 21.305 164.385   2488
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.65 %
    Favored  : 84.30 %
  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:  0.79 (0.50), residues: 331
  helix:  1.99 (0.41), residues: 174
  sheet:  1.09 (1.16), residues: 10
  loop : -1.40 (0.56), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 135 
 TYR   0.011   0.002   TYR A  76 
 PHE   0.009   0.001   PHE A  83 
 TRP   0.008   0.001   TRP A 120 
 HIS   0.003   0.001   HIS A 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6072)
  covalent geometry    : angle       0.58020 ( 8837)
  hydrogen bonds       : bond        0.04801 (  254)
  hydrogen bonds       : angle       3.43695 (  578)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 GLN cc_start: 0.9054 (mt0) cc_final: 0.8543 (mp10)
REVERT: A  579 LYS cc_start: 0.8548 (mtpt) cc_final: 0.8230 (mtpp)
REVERT: A  607 LEU cc_start: 0.5525 (OUTLIER) cc_final: 0.5145 (tt)
  outliers start: 6
  outliers final: 5
  residues processed: 47
  average time/residue: 0.1191
  time to fit residues: 6.7535
Evaluate side-chains
  48 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  649 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0270
   overall best weight:    1.2046

-------------------------------------------------------------------------------
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 = 0.4120 r_free = 0.4120 target = 0.141356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.097938 restraints weight = 11853.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.12
r_work: 0.3299 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6072  Z= 0.173
  Angle     :  0.581   9.463   8837  Z= 0.312
  Chirality :  0.040   0.649   1089
  Planarity :  0.004   0.035    621
  Dihedral  : 21.265 163.672   2488
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.99 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.83 (0.50), residues: 331
  helix:  2.06 (0.41), residues: 174
  sheet:  0.77 (1.02), residues: 10
  loop : -1.42 (0.57), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 152 
 TYR   0.012   0.002   TYR A  76 
 PHE   0.010   0.001   PHE A  83 
 TRP   0.009   0.002   TRP A 127 
 HIS   0.003   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 6072)
  covalent geometry    : angle       0.58106 ( 8837)
  hydrogen bonds       : bond        0.04882 (  254)
  hydrogen bonds       : angle       3.49553 (  578)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 TYR cc_start: 0.8715 (t80) cc_final: 0.8450 (t80)
REVERT: A   95 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7757 (p90)
REVERT: A  248 GLN cc_start: 0.9042 (mt0) cc_final: 0.8528 (mp10)
REVERT: A  579 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8239 (mtpp)
REVERT: A  607 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5456 (tt)
REVERT: A  649 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7991 (tmmt)
  outliers start: 7
  outliers final: 4
  residues processed: 46
  average time/residue: 0.1029
  time to fit residues: 5.7979
Evaluate side-chains
  50 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   95 TYR
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  649 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0060
   chunk 35 optimal weight:    8.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:   30.0000
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    1.1202

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.141400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.098096 restraints weight = 11887.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.14
r_work: 0.3304 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6072  Z= 0.162
  Angle     :  0.568   9.306   8837  Z= 0.305
  Chirality :  0.039   0.631   1089
  Planarity :  0.003   0.034    621
  Dihedral  : 21.261 162.389   2488
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 13.65 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.92 (0.51), residues: 331
  helix:  2.06 (0.41), residues: 176
  sheet:  0.61 (1.03), residues: 10
  loop : -1.29 (0.59), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 152 
 TYR   0.013   0.002   TYR A  76 
 PHE   0.009   0.001   PHE A 570 
 TRP   0.007   0.001   TRP A 120 
 HIS   0.003   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6072)
  covalent geometry    : angle       0.56843 ( 8837)
  hydrogen bonds       : bond        0.04651 (  254)
  hydrogen bonds       : angle       3.39071 (  578)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7724 (p90)
REVERT: A  228 ARG cc_start: 0.9050 (mmm160) cc_final: 0.8657 (mmm160)
REVERT: A  248 GLN cc_start: 0.9024 (mt0) cc_final: 0.8517 (mp10)
REVERT: A  579 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8241 (mtpp)
REVERT: A  607 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5542 (tt)
REVERT: A  649 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8025 (tmmt)
  outliers start: 8
  outliers final: 5
  residues processed: 48
  average time/residue: 0.1020
  time to fit residues: 6.0716
Evaluate side-chains
  51 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   95 TYR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  649 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:    0.4980
   chunk 13 optimal weight:    0.3980
   chunk 7 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0040
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.141517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.098016 restraints weight = 11674.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.13
r_work: 0.3308 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.4152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.122   6072  Z= 0.213
  Angle     :  1.001  59.199   8837  Z= 0.604
  Chirality :  0.042   0.629   1089
  Planarity :  0.004   0.037    621
  Dihedral  : 21.269 162.412   2488
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.31 %
    Favored  : 84.30 %
  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:  0.87 (0.51), residues: 331
  helix:  1.99 (0.41), residues: 176
  sheet:  0.62 (1.04), residues: 10
  loop : -1.29 (0.58), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 152 
 TYR   0.012   0.002   TYR A  76 
 PHE   0.008   0.001   PHE A 570 
 TRP   0.007   0.001   TRP A 120 
 HIS   0.002   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 6072)
  covalent geometry    : angle       1.00051 ( 8837)
  hydrogen bonds       : bond        0.04612 (  254)
  hydrogen bonds       : angle       3.39318 (  578)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1497.31 seconds
wall clock time: 26 minutes 25.22 seconds (1585.22 seconds total)