Starting phenix.real_space_refine
on Fri Oct 10 10:17:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vja_43278/10_2025/8vja_43278.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vja_43278/10_2025/8vja_43278.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vja_43278/10_2025/8vja_43278.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vja_43278/10_2025/8vja_43278.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vja_43278/10_2025/8vja_43278.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vja_43278/10_2025/8vja_43278.cif"
  }
  resolution = 2.7
  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=   0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1322      2.51       5
     N     357      2.21       5
     O     424      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2113
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2113
          Classifications: {'peptide': 275}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 8, 'TRANS': 266}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 22
  Time building chain proxies: 0.91, per 1000 atoms: 0.43
  Number of scatterers: 2113
  At special positions: 0
  Unit cell: (77.9, 104.14, 62.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     424      8.00
     N     357      7.00
     C    1322      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: 0.16
  Conformation dependent library (CDL) restraints added in 83.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  502

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 5 sheets defined
      5.1% alpha, 48.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 81 through 89
    Processing helix  chain 'A' and resid 152 through 156
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33
      removed outlier: 6.977A  pdb=" N   VAL A 213 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   SER A 237 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   GLY A 215 " --> pdb=" O   LYS A 235 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   LYS A 235 " --> pdb=" O   GLY A 215 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   SER A 221 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   LYS A 229 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LYS A 235 " --> pdb=" O   MET A 261 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   GLN A  71 " --> pdb=" O   ALA A 260 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   SER A  64 " --> pdb=" O   HIS A  51 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   HIS A  51 " --> pdb=" O   SER A  64 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   LEU A  66 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   LEU A  49 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLU A  68 " --> pdb=" O   GLU A  47 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ASP A  45 " --> pdb=" O   SER A  70 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33
      removed outlier: 6.977A  pdb=" N   VAL A 213 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   SER A 237 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   GLY A 215 " --> pdb=" O   LYS A 235 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   LYS A 235 " --> pdb=" O   GLY A 215 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   SER A 221 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   LYS A 229 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 97
    Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 108
      removed outlier: 5.604A  pdb=" N   TYR A 196 " --> pdb=" O   ASP A 103 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   LYS A 105 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL A 194 " --> pdb=" O   LYS A 105 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   VAL A 107 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ILE A 192 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ASN A 134 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 118
      removed outlier: 3.575A  pdb=" N   ARG A 115 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)

    78 hydrogen bonds defined for protein.
    204 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: 0.28

  Time building geometry restraints manager: 0.22 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 373
        1.30 -     1.43: 577
        1.43 -     1.56: 1183
        1.56 -     1.69: 0
        1.69 -     1.82: 19
  Bond restraints: 2152
  Sorted by residual:
  bond pdb=" C   ASN A 230 "
       pdb=" O   ASN A 230 "
    ideal  model  delta    sigma   weight residual
    1.234  1.167  0.068 1.22e-02 6.72e+03 3.07e+01
  bond pdb=" C   LYS A 229 "
       pdb=" O   LYS A 229 "
    ideal  model  delta    sigma   weight residual
    1.234  1.191  0.043 1.22e-02 6.72e+03 1.21e+01
  bond pdb=" CA  TYR A   5 "
       pdb=" C   TYR A   5 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 1.24e-02 6.50e+03 1.02e+01
  bond pdb=" C   ASP A  19 "
       pdb=" O   ASP A  19 "
    ideal  model  delta    sigma   weight residual
    1.235  1.202  0.034 1.14e-02 7.69e+03 8.67e+00
  bond pdb=" CZ  ARG A 269 "
       pdb=" NH2 ARG A 269 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 7.98e+00
  ... (remaining 2147 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 1963
        1.57 -     3.14: 757
        3.14 -     4.71: 166
        4.71 -     6.28: 35
        6.28 -     7.86: 6
  Bond angle restraints: 2927
  Sorted by residual:
  angle pdb=" N   ARG A 176 "
        pdb=" CA  ARG A 176 "
        pdb=" C   ARG A 176 "
      ideal   model   delta    sigma   weight residual
     108.90  116.76   -7.86 1.63e+00 3.76e-01 2.32e+01
  angle pdb=" N   HIS A  56 "
        pdb=" CA  HIS A  56 "
        pdb=" C   HIS A  56 "
      ideal   model   delta    sigma   weight residual
     108.99  116.43   -7.44 1.57e+00 4.06e-01 2.25e+01
  angle pdb=" C   ASP A 222 "
        pdb=" N   ASN A 223 "
        pdb=" CA  ASN A 223 "
      ideal   model   delta    sigma   weight residual
     120.65  126.89   -6.24 1.36e+00 5.41e-01 2.10e+01
  angle pdb=" N   ARG A 218 "
        pdb=" CA  ARG A 218 "
        pdb=" C   ARG A 218 "
      ideal   model   delta    sigma   weight residual
     108.48  115.80   -7.32 1.80e+00 3.09e-01 1.65e+01
  angle pdb=" N   TYR A   5 "
        pdb=" CA  TYR A   5 "
        pdb=" C   TYR A   5 "
      ideal   model   delta    sigma   weight residual
     109.24  102.47    6.77 1.67e+00 3.59e-01 1.64e+01
  ... (remaining 2922 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    16.25: 1134
       16.25 -    32.50: 101
       32.50 -    48.74: 26
       48.74 -    64.99: 6
       64.99 -    81.23: 1
  Dihedral angle restraints: 1268
    sinusoidal: 477
      harmonic: 791
  Sorted by residual:
  dihedral pdb=" CA  GLU A  68 "
           pdb=" C   GLU A  68 "
           pdb=" N   ALA A  69 "
           pdb=" CA  ALA A  69 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.88   28.12     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  LEU A  67 "
           pdb=" C   LEU A  67 "
           pdb=" N   GLU A  68 "
           pdb=" CA  GLU A  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.44   26.56     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CA  THR A  96 "
           pdb=" C   THR A  96 "
           pdb=" N   THR A  97 "
           pdb=" CA  THR A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.54   26.46     0      5.00e+00 4.00e-02 2.80e+01
  ... (remaining 1265 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 170
       0.065 -    0.130: 111
       0.130 -    0.195: 37
       0.195 -    0.259: 9
       0.259 -    0.324: 2
  Chirality restraints: 329
  Sorted by residual:
  chirality pdb=" CA  CYS A  77 "
            pdb=" N   CYS A  77 "
            pdb=" C   CYS A  77 "
            pdb=" CB  CYS A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CB  THR A  41 "
            pdb=" CA  THR A  41 "
            pdb=" OG1 THR A  41 "
            pdb=" CG2 THR A  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.27    0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CA  PRO A 164 "
            pdb=" N   PRO A 164 "
            pdb=" C   PRO A 164 "
            pdb=" CB  PRO A 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 326 not shown)

  Planarity restraints: 388
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 117 "   -0.087 2.00e-02 2.50e+03   4.71e-02 4.44e+01
        pdb=" CG  TYR A 117 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 117 "    0.048 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 117 "    0.041 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 117 "    0.021 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 117 "    0.027 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 117 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR A 117 "   -0.067 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 196 "    0.079 2.00e-02 2.50e+03   4.54e-02 4.12e+01
        pdb=" CG  TYR A 196 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 196 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 196 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 196 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 196 "   -0.033 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 196 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 196 "    0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A   9 "   -0.074 2.00e-02 2.50e+03   4.15e-02 3.45e+01
        pdb=" CG  TYR A   9 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR A   9 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR A   9 "    0.031 2.00e-02 2.50e+03
        pdb=" CE1 TYR A   9 "    0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR A   9 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ  TYR A   9 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A   9 "   -0.067 2.00e-02 2.50e+03
  ... (remaining 385 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 1049
        3.01 -     3.48: 1906
        3.48 -     3.95: 3287
        3.95 -     4.43: 3462
        4.43 -     4.90: 6216
  Nonbonded interactions: 15920
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 103 "
            pdb=" NE2 GLN A 195 "
     model   vdw
     2.535 3.120
  nonbonded pdb=" OD1 ASP A  19 "
            pdb=" O   ALA A 216 "
     model   vdw
     2.559 3.040
  nonbonded pdb=" OE1 GLU A 106 "
            pdb=" OH  TYR A 196 "
     model   vdw
     2.581 3.040
  nonbonded pdb=" OE2 GLU A  31 "
            pdb=" NH1 ARG A 218 "
     model   vdw
     2.583 3.120
  nonbonded pdb=" OG1 THR A 133 "
            pdb=" OD1 ASP A 199 "
     model   vdw
     2.587 3.040
  ... (remaining 15915 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             13.850
  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:             0.020
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.770
  Find NCS groups from input model:        0.010
  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:6.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.068   2152  Z= 0.695
  Angle     :  1.734   7.856   2927  Z= 1.137
  Chirality :  0.091   0.324    329
  Planarity :  0.010   0.047    388
  Dihedral  : 14.095  81.235    766
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  :  4.87 %
    Favored  : 91.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.74 (0.42), residues: 273
  helix: -0.74 (1.53), residues: 10
  sheet:  0.57 (0.46), residues: 95
  loop : -1.15 (0.39), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 269 
 TYR   0.087   0.018   TYR A 117 
 PHE   0.034   0.011   PHE A  18 
 TRP   0.057   0.018   TRP A  88 
 HIS   0.007   0.004   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.01158 ( 2152)
  covalent geometry    : angle       1.73375 ( 2927)
  hydrogen bonds       : bond        0.16178 (   66)
  hydrogen bonds       : angle       8.39536 (  204)

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

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

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 THR cc_start: 0.8290 (m) cc_final: 0.7815 (p)
REVERT: A   59 ARG cc_start: 0.8054 (mmt90) cc_final: 0.5465 (mtt180)
REVERT: A  259 LYS cc_start: 0.8431 (ttpt) cc_final: 0.7924 (tppt)
  outliers start: 9
  outliers final: 2
  residues processed: 59
  average time/residue: 0.6629
  time to fit residues: 39.7918
Evaluate side-chains
  33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 ARG
Chi-restraints excluded: chain A residue  195 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 9 optimal weight:    8.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.140630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.114614 restraints weight = 2964.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.71
r_work: 0.3393 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2152  Z= 0.126
  Angle     :  0.563   5.223   2927  Z= 0.325
  Chirality :  0.045   0.139    329
  Planarity :  0.004   0.030    388
  Dihedral  :  6.575  42.116    307
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 12.83 %
    Favored  : 80.97 %
  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: -0.47 (0.44), residues: 273
  helix:  0.55 (1.79), residues: 10
  sheet:  0.40 (0.42), residues: 106
  loop : -0.88 (0.43), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 269 
 TYR   0.009   0.001   TYR A   5 
 PHE   0.010   0.002   PHE A  75 
 TRP   0.006   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 2152)
  covalent geometry    : angle       0.56300 ( 2927)
  hydrogen bonds       : bond        0.03628 (   66)
  hydrogen bonds       : angle       5.98784 (  204)

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

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

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 33
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A  100 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6695 (tp40)
REVERT: A  137 MET cc_start: 0.8118 (ptp) cc_final: 0.7844 (ptm)
  outliers start: 14
  outliers final: 3
  residues processed: 44
  average time/residue: 0.5011
  time to fit residues: 22.5334
Evaluate side-chains
  34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  111 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    0.4980
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.137482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.108927 restraints weight = 2921.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.83
r_work: 0.3368 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2152  Z= 0.130
  Angle     :  0.527   4.906   2927  Z= 0.300
  Chirality :  0.045   0.139    329
  Planarity :  0.004   0.038    388
  Dihedral  :  5.132  14.774    300
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 14.60 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.44), residues: 273
  helix:  0.75 (1.85), residues: 10
  sheet:  0.30 (0.43), residues: 110
  loop : -0.97 (0.43), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 176 
 TYR   0.008   0.001   TYR A   5 
 PHE   0.007   0.001   PHE A 258 
 TRP   0.004   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 2152)
  covalent geometry    : angle       0.52706 ( 2927)
  hydrogen bonds       : bond        0.03318 (   66)
  hydrogen bonds       : angle       5.58888 (  204)

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

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

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 34
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A   27 ARG cc_start: 0.7432 (mtp180) cc_final: 0.7229 (mtp180)
REVERT: A   68 GLU cc_start: 0.8544 (pt0) cc_final: 0.8253 (pt0)
REVERT: A   71 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7715 (mt0)
REVERT: A  100 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6755 (tp40)
REVERT: A  130 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.5344 (mpp-170)
REVERT: A  195 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7728 (tt0)
  outliers start: 15
  outliers final: 5
  residues processed: 46
  average time/residue: 0.6060
  time to fit residues: 28.4413
Evaluate side-chains
  39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  195 GLN
Chi-restraints excluded: chain A residue  250 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   chunk 9 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0020
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0370
   chunk 11 optimal weight:    0.9990
   overall best weight:    1.2072

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

Flipped N/Q/H residues before XYZ refinement:
A 211 ASN
A 228 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.136848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.108203 restraints weight = 2876.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.81
r_work: 0.3359 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2152  Z= 0.137
  Angle     :  0.520   5.504   2927  Z= 0.293
  Chirality :  0.045   0.135    329
  Planarity :  0.004   0.058    388
  Dihedral  :  4.928  14.272    300
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 15.04 %
    Favored  : 77.88 %
  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: -0.46 (0.45), residues: 273
  helix:  0.70 (1.79), residues: 10
  sheet:  0.43 (0.46), residues: 102
  loop : -0.87 (0.43), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 176 
 TYR   0.007   0.001   TYR A   5 
 PHE   0.008   0.001   PHE A 258 
 TRP   0.003   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 2152)
  covalent geometry    : angle       0.51991 ( 2927)
  hydrogen bonds       : bond        0.03025 (   66)
  hydrogen bonds       : angle       5.50205 (  204)

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

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

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 31
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A   68 GLU cc_start: 0.8567 (pt0) cc_final: 0.8332 (pt0)
REVERT: A   71 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7750 (mt0)
REVERT: A  100 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6746 (tp40)
REVERT: A  129 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8183 (m)
REVERT: A  130 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.5406 (mpp-170)
  outliers start: 16
  outliers final: 4
  residues processed: 41
  average time/residue: 0.5579
  time to fit residues: 23.3220
Evaluate side-chains
  36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  183 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 14 optimal weight:    0.2980
   chunk 19 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.8588

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

Flipped N/Q/H residues before XYZ refinement:
A 211 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.137541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.109151 restraints weight = 2925.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.79
r_work: 0.3402 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2152  Z= 0.111
  Angle     :  0.486   5.081   2927  Z= 0.273
  Chirality :  0.044   0.131    329
  Planarity :  0.003   0.045    388
  Dihedral  :  4.528  13.451    300
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 15.93 %
    Favored  : 77.43 %
  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: -0.48 (0.46), residues: 273
  helix:  0.80 (1.77), residues: 10
  sheet:  0.37 (0.46), residues: 106
  loop : -0.88 (0.44), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 176 
 TYR   0.005   0.001   TYR A 244 
 PHE   0.007   0.001   PHE A 258 
 TRP   0.004   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 2152)
  covalent geometry    : angle       0.48557 ( 2927)
  hydrogen bonds       : bond        0.02709 (   66)
  hydrogen bonds       : angle       5.27049 (  204)

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

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

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 30
  time to evaluate  : 0.053 
Fit side-chains
REVERT: A   29 THR cc_start: 0.8276 (m) cc_final: 0.7888 (p)
REVERT: A   68 GLU cc_start: 0.8595 (pt0) cc_final: 0.7423 (tp30)
REVERT: A   97 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7641 (t)
REVERT: A  100 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6652 (tp40)
REVERT: A  130 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.5608 (mpp-170)
REVERT: A  205 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8310 (mp)
  outliers start: 15
  outliers final: 5
  residues processed: 40
  average time/residue: 0.5236
  time to fit residues: 21.3798
Evaluate side-chains
  37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  250 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 16 optimal weight:    0.2980
   chunk 12 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0970
   overall best weight:    2.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.134699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.104892 restraints weight = 2919.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 1.91
r_work: 0.3308 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   2152  Z= 0.260
  Angle     :  0.598   5.190   2927  Z= 0.330
  Chirality :  0.048   0.146    329
  Planarity :  0.004   0.043    388
  Dihedral  :  5.098  15.527    300
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  7.52 %
    Allowed  : 16.37 %
    Favored  : 76.11 %
  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: -0.61 (0.46), residues: 273
  helix:  0.50 (1.75), residues: 10
  sheet:  0.12 (0.46), residues: 106
  loop : -0.82 (0.45), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 176 
 TYR   0.010   0.002   TYR A 117 
 PHE   0.010   0.002   PHE A 258 
 TRP   0.003   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 2152)
  covalent geometry    : angle       0.59827 ( 2927)
  hydrogen bonds       : bond        0.03461 (   66)
  hydrogen bonds       : angle       5.77603 (  204)

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

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

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 29
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A   29 THR cc_start: 0.8366 (m) cc_final: 0.7932 (p)
REVERT: A   68 GLU cc_start: 0.8610 (pt0) cc_final: 0.7441 (tp30)
REVERT: A   97 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7748 (t)
REVERT: A  129 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8389 (m)
REVERT: A  130 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.5751 (mpp-170)
  outliers start: 17
  outliers final: 7
  residues processed: 42
  average time/residue: 0.5620
  time to fit residues: 24.0875
Evaluate side-chains
  37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  250 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.139592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.112165 restraints weight = 2994.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.82
r_work: 0.3374 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.3958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2152  Z= 0.116
  Angle     :  0.498   4.827   2927  Z= 0.277
  Chirality :  0.044   0.129    329
  Planarity :  0.003   0.038    388
  Dihedral  :  4.515  13.788    300
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 18.14 %
    Favored  : 76.55 %
  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: -0.55 (0.46), residues: 273
  helix:  0.94 (1.79), residues: 10
  sheet:  0.09 (0.46), residues: 106
  loop : -0.75 (0.45), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 176 
 TYR   0.007   0.001   TYR A 117 
 PHE   0.008   0.001   PHE A 258 
 TRP   0.003   0.001   TRP A 251 
 HIS   0.001   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 2152)
  covalent geometry    : angle       0.49791 ( 2927)
  hydrogen bonds       : bond        0.02643 (   66)
  hydrogen bonds       : angle       5.30582 (  204)

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

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

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 29
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A   29 THR cc_start: 0.8338 (m) cc_final: 0.7907 (p)
REVERT: A   68 GLU cc_start: 0.8547 (pt0) cc_final: 0.7420 (tp30)
REVERT: A  100 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6663 (tp40)
REVERT: A  129 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8225 (m)
REVERT: A  227 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8712 (mp)
  outliers start: 12
  outliers final: 5
  residues processed: 39
  average time/residue: 0.4839
  time to fit residues: 19.3313
Evaluate side-chains
  36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  250 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 8 optimal weight:    0.8980
   chunk 9 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   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 136 GLN
A 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.138774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.112206 restraints weight = 2913.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.69
r_work: 0.3378 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2152  Z= 0.121
  Angle     :  0.488   4.667   2927  Z= 0.272
  Chirality :  0.044   0.130    329
  Planarity :  0.003   0.035    388
  Dihedral  :  4.440  14.061    300
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 16.81 %
    Favored  : 76.11 %
  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: -0.45 (0.47), residues: 273
  helix:  1.03 (1.82), residues: 10
  sheet:  0.17 (0.47), residues: 104
  loop : -0.69 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 176 
 TYR   0.007   0.001   TYR A 244 
 PHE   0.007   0.001   PHE A 258 
 TRP   0.002   0.001   TRP A 251 
 HIS   0.001   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2152)
  covalent geometry    : angle       0.48772 ( 2927)
  hydrogen bonds       : bond        0.02598 (   66)
  hydrogen bonds       : angle       5.16221 (  204)

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

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

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 30
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A   29 THR cc_start: 0.8280 (m) cc_final: 0.7906 (p)
REVERT: A   68 GLU cc_start: 0.8556 (pt0) cc_final: 0.7488 (tp30)
REVERT: A   97 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7703 (t)
REVERT: A  100 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6681 (tp40)
REVERT: A  129 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8246 (m)
REVERT: A  209 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.6797 (mmtt)
REVERT: A  227 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8731 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 45
  average time/residue: 0.4000
  time to fit residues: 18.4405
Evaluate side-chains
  42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 29
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  250 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 15 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.138219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.111016 restraints weight = 2942.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 1.77
r_work: 0.3358 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2152  Z= 0.159
  Angle     :  0.508   4.627   2927  Z= 0.281
  Chirality :  0.044   0.135    329
  Planarity :  0.003   0.035    388
  Dihedral  :  4.543  14.159    300
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 18.14 %
    Favored  : 75.22 %
  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: -0.47 (0.47), residues: 273
  helix:  1.02 (1.84), residues: 10
  sheet:  0.11 (0.46), residues: 104
  loop : -0.66 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 176 
 TYR   0.009   0.001   TYR A 244 
 PHE   0.009   0.001   PHE A 258 
 TRP   0.002   0.001   TRP A  88 
 HIS   0.002   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 2152)
  covalent geometry    : angle       0.50783 ( 2927)
  hydrogen bonds       : bond        0.02788 (   66)
  hydrogen bonds       : angle       5.30944 (  204)

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

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

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 27
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A   29 THR cc_start: 0.8405 (m) cc_final: 0.8040 (p)
REVERT: A   68 GLU cc_start: 0.8567 (pt0) cc_final: 0.7429 (tp30)
REVERT: A   97 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7627 (t)
REVERT: A  100 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6639 (tp40)
REVERT: A  129 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8273 (m)
REVERT: A  130 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.5600 (mpp-170)
REVERT: A  209 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.6861 (mmtt)
REVERT: A  227 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8720 (mp)
  outliers start: 15
  outliers final: 6
  residues processed: 41
  average time/residue: 0.5113
  time to fit residues: 21.3581
Evaluate side-chains
  39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 27
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  250 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.137982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.109513 restraints weight = 3000.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.84
r_work: 0.3365 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2152  Z= 0.130
  Angle     :  0.493   4.609   2927  Z= 0.273
  Chirality :  0.044   0.132    329
  Planarity :  0.003   0.035    388
  Dihedral  :  4.463  13.887    300
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 19.91 %
    Favored  : 74.78 %
  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: -0.46 (0.47), residues: 273
  helix:  1.05 (1.83), residues: 10
  sheet:  0.13 (0.47), residues: 104
  loop : -0.66 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 176 
 TYR   0.009   0.001   TYR A 244 
 PHE   0.007   0.001   PHE A 258 
 TRP   0.002   0.001   TRP A  88 
 HIS   0.002   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 2152)
  covalent geometry    : angle       0.49281 ( 2927)
  hydrogen bonds       : bond        0.02622 (   66)
  hydrogen bonds       : angle       5.24694 (  204)

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

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

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  546 Ramachandran restraints generated.
    273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A   29 THR cc_start: 0.8392 (m) cc_final: 0.8036 (p)
REVERT: A   68 GLU cc_start: 0.8564 (pt0) cc_final: 0.7449 (tp30)
REVERT: A   97 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7610 (t)
REVERT: A  100 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6622 (tp40)
REVERT: A  129 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8223 (m)
REVERT: A  209 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.6832 (mmtt)
REVERT: A  227 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8722 (mp)
  outliers start: 12
  outliers final: 4
  residues processed: 40
  average time/residue: 0.4815
  time to fit residues: 19.6930
Evaluate side-chains
  38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  250 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    0.3980
   chunk 18 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.138887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.110695 restraints weight = 3060.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.85
r_work: 0.3386 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
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      :  0.002   0.031   2152  Z= 0.108
  Angle     :  0.472   4.558   2927  Z= 0.262
  Chirality :  0.044   0.151    329
  Planarity :  0.003   0.034    388
  Dihedral  :  4.277  13.225    300
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 19.91 %
    Favored  : 74.78 %
  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 (0.47), residues: 273
  helix:  1.11 (1.83), residues: 10
  sheet:  0.18 (0.48), residues: 104
  loop : -0.63 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 176 
 TYR   0.009   0.001   TYR A 244 
 PHE   0.007   0.001   PHE A 258 
 TRP   0.002   0.001   TRP A 251 
 HIS   0.001   0.000   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 2152)
  covalent geometry    : angle       0.47166 ( 2927)
  hydrogen bonds       : bond        0.02471 (   66)
  hydrogen bonds       : angle       5.08066 (  204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1467.16 seconds
wall clock time: 25 minutes 43.19 seconds (1543.19 seconds total)