Starting phenix.real_space_refine
on Fri May  9 15:38:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bgy_44526/05_2025/9bgy_44526.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bgy_44526/05_2025/9bgy_44526.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bgy_44526/05_2025/9bgy_44526.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bgy_44526/05_2025/9bgy_44526.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bgy_44526/05_2025/9bgy_44526.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bgy_44526/05_2025/9bgy_44526.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
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      20      5.16       5
     C    1931      2.51       5
     N     456      2.21       5
     O     509      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2916
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 2916
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 16, 'TRANS': 372}
  Time building chain proxies: 3.18, per 1000 atoms: 1.09
  Number of scatterers: 2916
  At special positions: 0
  Unit cell: (68.475, 61.875, 80.025, 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      20     16.00
     O     509      8.00
     N     456      7.00
     C    1931      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: 0.77
  Conformation dependent library (CDL) restraints added in 344.4 milliseconds
  

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  708

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 0 sheets defined
      90.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 22
    Processing helix  chain 'A' and resid 23 through 27
      removed outlier: 3.702A  pdb=" N   PHE A  27 " --> pdb=" O   LYS A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 41
      removed outlier: 3.838A  pdb=" N   GLY A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   PHE A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 59
      removed outlier: 3.786A  pdb=" N   GLY A  59 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 93
      removed outlier: 3.855A  pdb=" N   LEU A  64 " --> pdb=" O   ASP A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 121
    Processing helix  chain 'A' and resid 126 through 134
    Processing helix  chain 'A' and resid 135 through 154
      removed outlier: 3.581A  pdb=" N   GLY A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 180
      removed outlier: 3.705A  pdb=" N   LYS A 180 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 197
    Processing helix  chain 'A' and resid 198 through 203
    Processing helix  chain 'A' and resid 205 through 231
      removed outlier: 3.761A  pdb=" N   TYR A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   THR A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 243
    Processing helix  chain 'A' and resid 243 through 254
    Processing helix  chain 'A' and resid 255 through 271
      Proline residue:  A 261  - end of helix
    Processing helix  chain 'A' and resid 273 through 288
      removed outlier: 3.607A  pdb=" N   PHE A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      Proline residue:  A 282  - end of helix
      removed outlier: 3.856A  pdb=" N   THR A 286 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 307
      removed outlier: 3.559A  pdb=" N   ILE A 301 " --> pdb=" O   GLY A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 321
    Processing helix  chain 'A' and resid 322 through 327
    Processing helix  chain 'A' and resid 329 through 333
      removed outlier: 3.722A  pdb=" N   GLY A 332 " --> pdb=" O   GLY A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 349
    Processing helix  chain 'A' and resid 351 through 361
      removed outlier: 4.255A  pdb=" N   ILE A 355 " --> pdb=" O   PRO A 351 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE A 358 " --> pdb=" O   GLY A 354 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLY A 360 " --> pdb=" O   ALA A 356 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ILE A 361 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 387
      removed outlier: 3.509A  pdb=" N   LEU A 365 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ALA A 368 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)

    235 hydrogen bonds defined for protein.
    699 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: 0.84

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 889
        1.34 -     1.46: 598
        1.46 -     1.58: 1444
        1.58 -     1.69: 0
        1.69 -     1.81: 37
  Bond restraints: 2968
  Sorted by residual:
  bond pdb=" N   MET A   1 "
       pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.88e+00
  bond pdb=" C   ILE A 243 "
       pdb=" O   ILE A 243 "
    ideal  model  delta    sigma   weight residual
    1.236  1.228  0.008 1.19e-02 7.06e+03 4.82e-01
  bond pdb=" CA  ILE A 243 "
       pdb=" C   ILE A 243 "
    ideal  model  delta    sigma   weight residual
    1.523  1.531 -0.008 1.27e-02 6.20e+03 4.15e-01
  bond pdb=" N   VAL A 333 "
       pdb=" CA  VAL A 333 "
    ideal  model  delta    sigma   weight residual
    1.468  1.461  0.007 1.22e-02 6.72e+03 3.54e-01
  bond pdb=" CA  ILE A 222 "
       pdb=" CB  ILE A 222 "
    ideal  model  delta    sigma   weight residual
    1.540  1.548 -0.008 1.36e-02 5.41e+03 3.37e-01
  ... (remaining 2963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.93: 3834
        0.93 -     1.86: 155
        1.86 -     2.80: 20
        2.80 -     3.73: 15
        3.73 -     4.66: 9
  Bond angle restraints: 4033
  Sorted by residual:
  angle pdb=" N   THR A 286 "
        pdb=" CA  THR A 286 "
        pdb=" C   THR A 286 "
      ideal   model   delta    sigma   weight residual
     114.04  111.50    2.54 1.24e+00 6.50e-01 4.21e+00
  angle pdb=" N   ALA A 285 "
        pdb=" CA  ALA A 285 "
        pdb=" C   ALA A 285 "
      ideal   model   delta    sigma   weight residual
     113.01  110.68    2.33 1.20e+00 6.94e-01 3.77e+00
  angle pdb=" C   LEU A 321 "
        pdb=" N   THR A 322 "
        pdb=" CA  THR A 322 "
      ideal   model   delta    sigma   weight residual
     121.54  124.32   -2.78 1.91e+00 2.74e-01 2.12e+00
  angle pdb=" CB  ARG A 238 "
        pdb=" CG  ARG A 238 "
        pdb=" CD  ARG A 238 "
      ideal   model   delta    sigma   weight residual
     111.30  114.53   -3.23 2.30e+00 1.89e-01 1.97e+00
  angle pdb=" N   ILE A  42 "
        pdb=" CA  ILE A  42 "
        pdb=" CB  ILE A  42 "
      ideal   model   delta    sigma   weight residual
     112.07  109.95    2.12 1.52e+00 4.33e-01 1.95e+00
  ... (remaining 4028 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.51: 1572
       16.51 -    33.02: 145
       33.02 -    49.53: 41
       49.53 -    66.04: 8
       66.04 -    82.55: 1
  Dihedral angle restraints: 1767
    sinusoidal: 662
      harmonic: 1105
  Sorted by residual:
  dihedral pdb=" CG  ARG A  37 "
           pdb=" CD  ARG A  37 "
           pdb=" NE  ARG A  37 "
           pdb=" CZ  ARG A  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.69   44.69     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CG  ARG A 369 "
           pdb=" CD  ARG A 369 "
           pdb=" NE  ARG A 369 "
           pdb=" CZ  ARG A 369 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -136.56  -43.44     2      1.50e+01 4.44e-03 1.01e+01
  dihedral pdb=" CB  MET A 289 "
           pdb=" CG  MET A 289 "
           pdb=" SD  MET A 289 "
           pdb=" CE  MET A 289 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.66   57.34     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 1764 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 331
       0.027 -    0.055: 107
       0.055 -    0.082: 59
       0.082 -    0.110: 14
       0.110 -    0.137: 3
  Chirality restraints: 514
  Sorted by residual:
  chirality pdb=" CA  ILE A 123 "
            pdb=" N   ILE A 123 "
            pdb=" C   ILE A 123 "
            pdb=" CB  ILE A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CA  VAL A 272 "
            pdb=" N   VAL A 272 "
            pdb=" C   VAL A 272 "
            pdb=" CB  VAL A 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.62e-01
  chirality pdb=" CA  VAL A 333 "
            pdb=" N   VAL A 333 "
            pdb=" C   VAL A 333 "
            pdb=" CB  VAL A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.18e-01
  ... (remaining 511 not shown)

  Planarity restraints: 488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 322 "   -0.020 2.00e-02 2.50e+03   3.91e-02 1.53e+01
        pdb=" C   THR A 322 "    0.068 2.00e-02 2.50e+03
        pdb=" O   THR A 322 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   ALA A 323 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  27 "   -0.007 2.00e-02 2.50e+03   9.33e-03 1.52e+00
        pdb=" CG  PHE A  27 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  27 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  27 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  27 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  27 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  27 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 272 "   -0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO A 273 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A 273 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 273 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 485 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 51
        2.70 -     3.25: 3207
        3.25 -     3.80: 4819
        3.80 -     4.35: 5919
        4.35 -     4.90: 10177
  Nonbonded interactions: 24173
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 321 "
            pdb=" OG1 THR A 322 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" OD1 ASP A 366 "
            pdb=" NH2 ARG A 369 "
     model   vdw
     2.194 3.120
  nonbonded pdb=" OH  TYR A 224 "
            pdb=" OD2 ASP A 290 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   LEU A  87 "
            pdb=" ND2 ASN A  91 "
     model   vdw
     2.463 3.120
  nonbonded pdb=" O   LEU A  46 "
            pdb=" OG1 THR A  50 "
     model   vdw
     2.474 3.040
  ... (remaining 24168 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:             2.090
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.140
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
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      :  0.003   0.032   2968  Z= 0.130
  Angle     :  0.500   4.660   4033  Z= 0.269
  Chirality :  0.036   0.137    514
  Planarity :  0.003   0.039    488
  Dihedral  : 14.215  82.551   1059
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 14.97 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.93 (0.44), residues: 387
  helix:  2.15 (0.28), residues: 335
  sheet:  None (None), residues: 0
  loop :  0.71 (1.10), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 192 
 HIS   0.002   0.001   HIS A 219 
 PHE   0.021   0.001   PHE A  27 
 TYR   0.006   0.001   TYR A 184 
 ARG   0.001   0.000   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11231 (  235)
  hydrogen bonds       : angle       5.18952 (  699)
  covalent geometry    : bond        0.00269 ( 2968)
  covalent geometry    : angle       0.49955 ( 4033)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.8310 (mttm) cc_final: 0.8009 (mttp)
REVERT: A   26 GLU cc_start: 0.7418 (tp30) cc_final: 0.7150 (tp30)
REVERT: A   61 VAL cc_start: 0.8326 (m) cc_final: 0.8088 (t)
REVERT: A   62 LYS cc_start: 0.8402 (mttt) cc_final: 0.8132 (mtpm)
REVERT: A   63 LYS cc_start: 0.8217 (tttt) cc_final: 0.7852 (tttm)
REVERT: A   94 LYS cc_start: 0.7874 (mttt) cc_final: 0.7673 (mttp)
REVERT: A  131 MET cc_start: 0.8474 (tpp) cc_final: 0.8170 (mmt)
REVERT: A  158 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7442 (mm-30)
REVERT: A  237 LEU cc_start: 0.8443 (tp) cc_final: 0.8176 (tm)
REVERT: A  241 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8235 (ttmt)
REVERT: A  288 ASN cc_start: 0.8885 (t0) cc_final: 0.8657 (t0)
REVERT: A  289 MET cc_start: 0.8199 (mmp) cc_final: 0.7768 (mmt)
REVERT: A  325 LEU cc_start: 0.8048 (tm) cc_final: 0.7824 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 87
  average time/residue: 1.2506
  time to fit residues: 111.4314
Evaluate side-chains
  75 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.4980
   chunk 28 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0270
   chunk 9 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    0.4980
   chunk 34 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
A 111 ASN
A 296 GLN
A 305 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.096054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.085064 restraints weight = 4734.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.58
r_work: 0.3049 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2968  Z= 0.167
  Angle     :  0.601   6.541   4033  Z= 0.298
  Chirality :  0.041   0.133    514
  Planarity :  0.004   0.040    488
  Dihedral  :  3.919  17.438    407
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 16.56 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.87 (0.44), residues: 387
  helix:  2.09 (0.28), residues: 334
  sheet:  None (None), residues: 0
  loop :  0.88 (1.06), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 192 
 HIS   0.003   0.001   HIS A 219 
 PHE   0.014   0.002   PHE A 164 
 TYR   0.008   0.002   TYR A   4 
 ARG   0.002   0.000   ARG A 369 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03873 (  235)
  hydrogen bonds       : angle       4.64538 (  699)
  covalent geometry    : bond        0.00403 ( 2968)
  covalent geometry    : angle       0.60062 ( 4033)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7866 (tp30) cc_final: 0.7475 (tp30)
REVERT: A   61 VAL cc_start: 0.8612 (m) cc_final: 0.8336 (t)
REVERT: A   63 LYS cc_start: 0.8498 (tttt) cc_final: 0.8265 (ttpt)
REVERT: A  131 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8355 (mmt)
REVERT: A  153 MET cc_start: 0.6328 (mtt) cc_final: 0.5916 (mtp)
REVERT: A  237 LEU cc_start: 0.8759 (tp) cc_final: 0.8527 (tm)
REVERT: A  312 THR cc_start: 0.8218 (p) cc_final: 0.7964 (p)
REVERT: A  325 LEU cc_start: 0.8338 (tm) cc_final: 0.7983 (mm)
  outliers start: 15
  outliers final: 5
  residues processed: 87
  average time/residue: 1.1804
  time to fit residues: 105.2507
Evaluate side-chains
  77 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  111 ASN
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  276 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 7 optimal weight:    0.2980
   chunk 28 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    0.1980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.097729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.086436 restraints weight = 4590.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 1.60
r_work: 0.3061 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   2968  Z= 0.186
  Angle     :  0.602   6.184   4033  Z= 0.301
  Chirality :  0.041   0.129    514
  Planarity :  0.004   0.037    488
  Dihedral  :  4.213  19.324    407
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 18.15 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.44), residues: 387
  helix:  1.92 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop :  0.59 (1.03), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP A 192 
 HIS   0.003   0.001   HIS A 219 
 PHE   0.016   0.002   PHE A 164 
 TYR   0.010   0.002   TYR A 307 
 ARG   0.001   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03847 (  235)
  hydrogen bonds       : angle       4.65766 (  699)
  covalent geometry    : bond        0.00462 ( 2968)
  covalent geometry    : angle       0.60218 ( 4033)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7847 (tp30) cc_final: 0.7465 (tp30)
REVERT: A   29 LYS cc_start: 0.8405 (tttp) cc_final: 0.8191 (tttm)
REVERT: A   61 VAL cc_start: 0.8660 (m) cc_final: 0.8356 (t)
REVERT: A  131 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8386 (mmt)
REVERT: A  153 MET cc_start: 0.6303 (mtt) cc_final: 0.5871 (mtp)
REVERT: A  255 SER cc_start: 0.8823 (p) cc_final: 0.8524 (p)
REVERT: A  312 THR cc_start: 0.8200 (p) cc_final: 0.7939 (p)
REVERT: A  325 LEU cc_start: 0.8438 (tm) cc_final: 0.8037 (mm)
  outliers start: 14
  outliers final: 5
  residues processed: 83
  average time/residue: 1.0133
  time to fit residues: 86.6864
Evaluate side-chains
  80 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  111 ASN
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  292 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 15 optimal weight:    0.3980
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0980
   chunk 33 optimal weight:    0.4980
   chunk 10 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.095874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.084463 restraints weight = 4614.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.59
r_work: 0.3034 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2968  Z= 0.177
  Angle     :  0.596   5.848   4033  Z= 0.297
  Chirality :  0.041   0.128    514
  Planarity :  0.004   0.035    488
  Dihedral  :  4.512  31.312    407
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 18.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.43), residues: 387
  helix:  1.89 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop :  0.39 (1.01), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP A 192 
 HIS   0.003   0.001   HIS A 219 
 PHE   0.015   0.002   PHE A 164 
 TYR   0.010   0.002   TYR A 307 
 ARG   0.001   0.000   ARG A 369 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03718 (  235)
  hydrogen bonds       : angle       4.67389 (  699)
  covalent geometry    : bond        0.00436 ( 2968)
  covalent geometry    : angle       0.59558 ( 4033)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   21 PHE cc_start: 0.8539 (m-10) cc_final: 0.8292 (m-10)
REVERT: A   26 GLU cc_start: 0.7862 (tp30) cc_final: 0.7461 (tp30)
REVERT: A   29 LYS cc_start: 0.8425 (tttp) cc_final: 0.8212 (tttm)
REVERT: A   61 VAL cc_start: 0.8657 (m) cc_final: 0.8336 (t)
REVERT: A   72 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8323 (mp)
REVERT: A  131 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8333 (mmt)
REVERT: A  153 MET cc_start: 0.6260 (mtt) cc_final: 0.5848 (mtp)
REVERT: A  255 SER cc_start: 0.8882 (p) cc_final: 0.8565 (p)
REVERT: A  312 THR cc_start: 0.8145 (p) cc_final: 0.7866 (p)
REVERT: A  325 LEU cc_start: 0.8455 (tm) cc_final: 0.8098 (mm)
  outliers start: 17
  outliers final: 5
  residues processed: 83
  average time/residue: 1.0790
  time to fit residues: 92.1624
Evaluate side-chains
  78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  292 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 13 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0060
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 111 ASN
A 305 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.096124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.084629 restraints weight = 4631.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.62
r_work: 0.3030 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2968  Z= 0.181
  Angle     :  0.597   5.843   4033  Z= 0.299
  Chirality :  0.041   0.127    514
  Planarity :  0.004   0.034    488
  Dihedral  :  4.194  18.809    405
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 19.75 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.44), residues: 387
  helix:  1.89 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop :  0.28 (1.02), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP A 192 
 HIS   0.003   0.001   HIS A 219 
 PHE   0.016   0.002   PHE A 164 
 TYR   0.010   0.002   TYR A 307 
 ARG   0.002   0.000   ARG A 369 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03722 (  235)
  hydrogen bonds       : angle       4.68373 (  699)
  covalent geometry    : bond        0.00446 ( 2968)
  covalent geometry    : angle       0.59730 ( 4033)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7876 (tp30) cc_final: 0.7468 (tp30)
REVERT: A   29 LYS cc_start: 0.8417 (tttp) cc_final: 0.8198 (tttm)
REVERT: A   61 VAL cc_start: 0.8660 (m) cc_final: 0.8327 (t)
REVERT: A  131 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8345 (mmt)
REVERT: A  153 MET cc_start: 0.6307 (mtt) cc_final: 0.5891 (mtp)
REVERT: A  211 THR cc_start: 0.8903 (t) cc_final: 0.8577 (p)
REVERT: A  255 SER cc_start: 0.8886 (p) cc_final: 0.8559 (p)
REVERT: A  312 THR cc_start: 0.8157 (p) cc_final: 0.7879 (p)
REVERT: A  325 LEU cc_start: 0.8475 (tm) cc_final: 0.8110 (mm)
  outliers start: 14
  outliers final: 6
  residues processed: 81
  average time/residue: 1.0742
  time to fit residues: 89.4031
Evaluate side-chains
  80 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  292 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 8 optimal weight:    0.1980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.095318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.083821 restraints weight = 4675.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.60
r_work: 0.3016 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   2968  Z= 0.237
  Angle     :  0.636   6.189   4033  Z= 0.320
  Chirality :  0.043   0.129    514
  Planarity :  0.004   0.034    488
  Dihedral  :  4.399  18.696    405
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 21.97 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.43), residues: 387
  helix:  1.73 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop :  0.13 (1.00), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 192 
 HIS   0.004   0.001   HIS A 219 
 PHE   0.018   0.002   PHE A 164 
 TYR   0.015   0.002   TYR A 307 
 ARG   0.002   0.000   ARG A 369 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  235)
  hydrogen bonds       : angle       4.81100 (  699)
  covalent geometry    : bond        0.00587 ( 2968)
  covalent geometry    : angle       0.63570 ( 4033)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7924 (tp30) cc_final: 0.7493 (tp30)
REVERT: A   29 LYS cc_start: 0.8437 (tttp) cc_final: 0.8197 (tttm)
REVERT: A   61 VAL cc_start: 0.8687 (m) cc_final: 0.8336 (t)
REVERT: A  131 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8323 (mmt)
REVERT: A  153 MET cc_start: 0.6433 (mtt) cc_final: 0.6032 (mtp)
REVERT: A  211 THR cc_start: 0.8894 (t) cc_final: 0.8567 (p)
REVERT: A  255 SER cc_start: 0.8877 (p) cc_final: 0.8553 (p)
REVERT: A  325 LEU cc_start: 0.8547 (tm) cc_final: 0.8194 (mm)
  outliers start: 10
  outliers final: 6
  residues processed: 77
  average time/residue: 1.0011
  time to fit residues: 79.4361
Evaluate side-chains
  77 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  292 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 16 optimal weight:    0.1980
   chunk 8 optimal weight:    0.4980
   chunk 37 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   chunk 13 optimal weight:    0.4980
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.096377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.084960 restraints weight = 4701.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.60
r_work: 0.3038 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2968  Z= 0.173
  Angle     :  0.607   6.257   4033  Z= 0.303
  Chirality :  0.041   0.136    514
  Planarity :  0.004   0.035    488
  Dihedral  :  4.299  19.399    405
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 23.57 %
    Favored  : 73.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.44), residues: 387
  helix:  1.87 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop :  0.17 (1.02), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 192 
 HIS   0.002   0.001   HIS A 219 
 PHE   0.015   0.002   PHE A 164 
 TYR   0.010   0.002   TYR A 307 
 ARG   0.001   0.000   ARG A 265 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03686 (  235)
  hydrogen bonds       : angle       4.71239 (  699)
  covalent geometry    : bond        0.00423 ( 2968)
  covalent geometry    : angle       0.60667 ( 4033)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7867 (tp30) cc_final: 0.7455 (tp30)
REVERT: A   29 LYS cc_start: 0.8419 (tttp) cc_final: 0.8209 (tttm)
REVERT: A   61 VAL cc_start: 0.8682 (m) cc_final: 0.8329 (t)
REVERT: A  131 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8309 (mmt)
REVERT: A  153 MET cc_start: 0.6318 (mtt) cc_final: 0.5931 (mtp)
REVERT: A  255 SER cc_start: 0.8882 (p) cc_final: 0.8549 (p)
REVERT: A  325 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8168 (mm)
  outliers start: 10
  outliers final: 6
  residues processed: 78
  average time/residue: 1.1269
  time to fit residues: 90.3063
Evaluate side-chains
  80 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  325 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 17 optimal weight:    0.0570
   chunk 28 optimal weight:    0.2980
   chunk 19 optimal weight:    0.7980
   chunk 21 optimal weight:    0.2980
   chunk 23 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 0 optimal weight:    0.0980
   overall best weight:    0.2698

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.099734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.088350 restraints weight = 4574.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.58
r_work: 0.3089 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2968  Z= 0.139
  Angle     :  0.600   6.706   4033  Z= 0.294
  Chirality :  0.040   0.131    514
  Planarity :  0.004   0.035    488
  Dihedral  :  4.179  19.413    405
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 24.20 %
    Favored  : 72.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.44), residues: 387
  helix:  2.04 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop :  0.06 (1.01), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 192 
 HIS   0.002   0.001   HIS A 219 
 PHE   0.011   0.001   PHE A 164 
 TYR   0.008   0.002   TYR A   4 
 ARG   0.001   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03446 (  235)
  hydrogen bonds       : angle       4.60120 (  699)
  covalent geometry    : bond        0.00333 ( 2968)
  covalent geometry    : angle       0.59989 ( 4033)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7822 (tp30) cc_final: 0.7420 (tp30)
REVERT: A   61 VAL cc_start: 0.8647 (m) cc_final: 0.8341 (t)
REVERT: A  131 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8333 (mmt)
REVERT: A  153 MET cc_start: 0.6264 (mtt) cc_final: 0.5902 (mtp)
REVERT: A  312 THR cc_start: 0.8085 (p) cc_final: 0.7801 (p)
REVERT: A  325 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8184 (mm)
  outliers start: 10
  outliers final: 7
  residues processed: 77
  average time/residue: 1.1637
  time to fit residues: 92.0337
Evaluate side-chains
  79 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  325 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   chunk 12 optimal weight:    0.0870
   chunk 4 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0970
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0770
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.2314

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.100419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.089033 restraints weight = 4581.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.59
r_work: 0.3102 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2968  Z= 0.135
  Angle     :  0.602   7.350   4033  Z= 0.296
  Chirality :  0.040   0.127    514
  Planarity :  0.004   0.035    488
  Dihedral  :  4.122  19.531    405
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 23.57 %
    Favored  : 72.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.75 (0.44), residues: 387
  helix:  2.11 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop :  0.10 (1.02), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 192 
 HIS   0.002   0.001   HIS A 219 
 PHE   0.011   0.001   PHE A 164 
 TYR   0.008   0.002   TYR A   4 
 ARG   0.001   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03387 (  235)
  hydrogen bonds       : angle       4.54178 (  699)
  covalent geometry    : bond        0.00321 ( 2968)
  covalent geometry    : angle       0.60234 ( 4033)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7779 (tp30) cc_final: 0.7374 (tp30)
REVERT: A   61 VAL cc_start: 0.8643 (m) cc_final: 0.8328 (t)
REVERT: A  131 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8333 (mmt)
REVERT: A  153 MET cc_start: 0.6263 (mtt) cc_final: 0.5913 (mtp)
REVERT: A  264 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7693 (mtt)
REVERT: A  312 THR cc_start: 0.8076 (p) cc_final: 0.7797 (p)
REVERT: A  313 LEU cc_start: 0.8818 (tm) cc_final: 0.8454 (tt)
REVERT: A  325 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8133 (mm)
  outliers start: 12
  outliers final: 5
  residues processed: 78
  average time/residue: 1.0505
  time to fit residues: 84.3148
Evaluate side-chains
  75 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0980
   chunk 9 optimal weight:    0.0770
   chunk 27 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0980
   chunk 20 optimal weight:    0.0570
   chunk 36 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 28 optimal weight:    0.4980
   overall best weight:    0.1656

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.099269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.087800 restraints weight = 4684.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 1.62
r_work: 0.3086 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2968  Z= 0.129
  Angle     :  0.610   7.663   4033  Z= 0.296
  Chirality :  0.040   0.129    514
  Planarity :  0.004   0.036    488
  Dihedral  :  4.112  19.208    405
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 25.48 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.92 (0.44), residues: 387
  helix:  2.22 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop :  0.23 (1.02), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 192 
 HIS   0.001   0.000   HIS A 219 
 PHE   0.010   0.001   PHE A  11 
 TYR   0.010   0.002   TYR A   4 
 ARG   0.001   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03256 (  235)
  hydrogen bonds       : angle       4.48277 (  699)
  covalent geometry    : bond        0.00303 ( 2968)
  covalent geometry    : angle       0.61021 ( 4033)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7747 (tp30) cc_final: 0.7313 (tp30)
REVERT: A   61 VAL cc_start: 0.8618 (m) cc_final: 0.8296 (t)
REVERT: A  131 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8333 (mmt)
REVERT: A  153 MET cc_start: 0.6216 (mtt) cc_final: 0.5891 (mtp)
REVERT: A  264 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7682 (mtt)
REVERT: A  312 THR cc_start: 0.8030 (p) cc_final: 0.7711 (p)
REVERT: A  313 LEU cc_start: 0.8802 (tm) cc_final: 0.8431 (tt)
REVERT: A  325 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8007 (mm)
  outliers start: 9
  outliers final: 3
  residues processed: 75
  average time/residue: 1.2178
  time to fit residues: 93.9494
Evaluate side-chains
  76 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 16 optimal weight:    0.2980
   chunk 8 optimal weight:    0.4980
   chunk 17 optimal weight:    0.2980
   chunk 4 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0470
   chunk 27 optimal weight:    0.3980
   chunk 34 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0980
   overall best weight:    0.2278

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.100524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.089025 restraints weight = 4565.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.59
r_work: 0.3110 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2968  Z= 0.137
  Angle     :  0.613   7.705   4033  Z= 0.299
  Chirality :  0.040   0.129    514
  Planarity :  0.004   0.036    488
  Dihedral  :  4.089  19.178    405
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 27.07 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.87 (0.44), residues: 387
  helix:  2.19 (0.28), residues: 332
  sheet:  None (None), residues: 0
  loop :  0.21 (1.01), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP A 192 
 HIS   0.001   0.001   HIS A 219 
 PHE   0.031   0.002   PHE A  27 
 TYR   0.008   0.002   TYR A   4 
 ARG   0.001   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03296 (  235)
  hydrogen bonds       : angle       4.49088 (  699)
  covalent geometry    : bond        0.00329 ( 2968)
  covalent geometry    : angle       0.61331 ( 4033)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2757.96 seconds
wall clock time: 48 minutes 16.85 seconds (2896.85 seconds total)