Starting phenix.real_space_refine
on Thu Jul 24 07:33:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fkq_50525/07_2025/9fkq_50525.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fkq_50525/07_2025/9fkq_50525.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fkq_50525/07_2025/9fkq_50525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fkq_50525/07_2025/9fkq_50525.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fkq_50525/07_2025/9fkq_50525.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fkq_50525/07_2025/9fkq_50525.cif"
  }
  resolution = 2.45
  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=   0.000 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    1816      2.51       5
     N     456      2.21       5
     O     540      1.98       5
     H    2784      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5602
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5602
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 362, 5577
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 21, 'TRANS': 340}
      Conformer: "B"
        Number of residues, atoms: 362, 5577
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 21, 'TRANS': 340}
          bond proxies already assigned to first conformer: 5618
  Time building chain proxies: 5.87, per 1000 atoms: 1.05
  Number of scatterers: 5602
  At special positions: 0
  Unit cell: (81.03, 59.13, 67.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       6     16.00
     O     540      8.00
     N     456      7.00
     C    1816      6.00
     H    2784      1.00
    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: 1.40
  Conformation dependent library (CDL) restraints added in 904.1 milliseconds
  

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  672

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 5 sheets defined
      52.8% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 32
    Processing helix  chain 'A' and resid 42 through 52
      Proline residue:  A  48  - end of helix
    Processing helix  chain 'A' and resid 64 through 73
      removed outlier: 3.554A  pdb=" N   GLY A  68 " --> pdb=" O   HIS A  64 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   GLY A  69 " --> pdb=" O   ASP A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 87
    Processing helix  chain 'A' and resid 90 through 97
      removed outlier: 3.713A  pdb=" N   VAL A  97 " --> pdb=" O   THR A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 142
      removed outlier: 4.680A  pdb=" N   ALA A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS A 137 " --> pdb=" O   PRO A 133 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 162
      removed outlier: 3.564A  pdb=" N   THR A 157 " --> pdb=" O   GLU A 153 " (cutoff:3.500A)
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 185 through 201
    Processing helix  chain 'A' and resid 209 through 219
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 231 through 239
    Processing helix  chain 'A' and resid 272 through 283
    Processing helix  chain 'A' and resid 286 through 297
      removed outlier: 3.650A  pdb=" N   ASP A 296 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 312
      removed outlier: 3.685A  pdb=" N   GLU A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 327
    Processing helix  chain 'A' and resid 335 through 352
      removed outlier: 3.529A  pdb=" N   ARG A 344 " --> pdb=" O   TRP A 340 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR A 345 " --> pdb=" O   TYR A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 366
      removed outlier: 3.772A  pdb=" N   THR A 366 " --> pdb=" O   LYS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38
      removed outlier: 6.753A  pdb=" N   GLY A 260 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   VAL A 110 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU A 262 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA A 301 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38
    Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99
    Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 147
      removed outlier: 8.264A  pdb=" N   SER A 145 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   THR A 225 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   LEU A 147 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 11.384A  pdb=" N   ASN A 227 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ALA A 223 " --> pdb=" O   ASN A 118 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 172
      removed outlier: 4.074A  pdb=" N   LYS A 170 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)

    145 hydrogen bonds defined for protein.
    419 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: 2.00

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2784
        1.03 -     1.23: 0
        1.23 -     1.42: 1194
        1.42 -     1.61: 1684
        1.61 -     1.81: 12
  Bond restraints: 5674
  Sorted by residual:
  bond pdb=" C   GLY A 252 "
       pdb=" N   GLN A 253 "
    ideal  model  delta    sigma   weight residual
    1.331  1.358 -0.027 2.07e-02 2.33e+03 1.65e+00
  bond pdb=" CA  ILE A 132 "
       pdb=" CB  ILE A 132 "
    ideal  model  delta    sigma   weight residual
    1.539  1.534  0.005 5.40e-03 3.43e+04 9.27e-01
  bond pdb=" CA  ASN A 100 "
       pdb=" CB  ASN A 100 "
    ideal  model  delta    sigma   weight residual
    1.529  1.541 -0.012 1.62e-02 3.81e+03 5.09e-01
  bond pdb=" CB  ASN A 100 "
       pdb=" CG  ASN A 100 "
    ideal  model  delta    sigma   weight residual
    1.516  1.533 -0.017 2.50e-02 1.60e+03 4.40e-01
  bond pdb=" CA  GLY A 260 "
       pdb=" C   GLY A 260 "
    ideal  model  delta    sigma   weight residual
    1.514  1.520 -0.005 8.20e-03 1.49e+04 4.24e-01
  ... (remaining 5669 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.75: 8906
        0.75 -     1.50: 1245
        1.50 -     2.25: 129
        2.25 -     3.00: 13
        3.00 -     3.75: 17
  Bond angle restraints: 10310
  Sorted by residual:
  angle pdb=" N   ASN A 100 "
        pdb=" CA  ASN A 100 "
        pdb=" C   ASN A 100 "
      ideal   model   delta    sigma   weight residual
     111.54  109.32    2.22 1.36e+00 5.41e-01 2.66e+00
  angle pdb=" CA  ASN A 100 "
        pdb=" CB  ASN A 100 "
        pdb=" CG  ASN A 100 "
      ideal   model   delta    sigma   weight residual
     112.60  114.07   -1.47 1.00e+00 1.00e+00 2.15e+00
  angle pdb=" CA  GLU A 309 "
        pdb=" CB  GLU A 309 "
        pdb=" CG  GLU A 309 "
      ideal   model   delta    sigma   weight residual
     114.10  116.97   -2.87 2.00e+00 2.50e-01 2.06e+00
  angle pdb=" C   PHE A  61 "
        pdb=" N   TRP A  62 "
        pdb=" CA  TRP A  62 "
      ideal   model   delta    sigma   weight residual
     122.09  119.56    2.53 1.86e+00 2.89e-01 1.85e+00
  angle pdb=" C   MET A 224 "
        pdb=" N   THR A 225 "
        pdb=" CA  THR A 225 "
      ideal   model   delta    sigma   weight residual
     121.87  124.02   -2.15 1.64e+00 3.72e-01 1.72e+00
  ... (remaining 10305 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 2481
       17.09 -    34.17: 141
       34.17 -    51.26: 41
       51.26 -    68.34: 19
       68.34 -    85.43: 3
  Dihedral angle restraints: 2685
    sinusoidal: 1439
      harmonic: 1246
  Sorted by residual:
  dihedral pdb=" CB  GLU A 131 "
           pdb=" CG  GLU A 131 "
           pdb=" CD  GLU A 131 "
           pdb=" OE1 GLU A 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.43   85.43     1      3.00e+01 1.11e-03 9.82e+00
  dihedral pdb=" CG  LYS A  34 "
           pdb=" CD  LYS A  34 "
           pdb=" CE  LYS A  34 "
           pdb=" NZ  LYS A  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  110.88  -50.88     3      1.50e+01 4.44e-03 8.95e+00
  dihedral pdb=" CA  ASP A  58 "
           pdb=" CB  ASP A  58 "
           pdb=" CG  ASP A  58 "
           pdb=" OD1 ASP A  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.92   50.92     1      2.00e+01 2.50e-03 8.87e+00
  ... (remaining 2682 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 256
       0.026 -    0.051: 115
       0.051 -    0.077: 22
       0.077 -    0.102: 15
       0.102 -    0.128: 18
  Chirality restraints: 426
  Sorted by residual:
  chirality pdb=" CA  ILE A 116 "
            pdb=" N   ILE A 116 "
            pdb=" C   ILE A 116 "
            pdb=" CB  ILE A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  VAL A  35 "
            pdb=" N   VAL A  35 "
            pdb=" C   VAL A  35 "
            pdb=" CB  VAL A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  VAL A   8 "
            pdb=" N   VAL A   8 "
            pdb=" C   VAL A   8 "
            pdb=" CB  VAL A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.85e-01
  ... (remaining 423 not shown)

  Planarity restraints: 854
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 270 "    0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO A 271 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  47 "    0.025 5.00e-02 4.00e+02   3.71e-02 2.20e+00
        pdb=" N   PRO A  48 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A  48 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  48 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 132 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 133 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 133 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 133 "    0.018 5.00e-02 4.00e+02
  ... (remaining 851 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 591
        2.25 -     2.84: 13058
        2.84 -     3.42: 15231
        3.42 -     4.01: 20833
        4.01 -     4.60: 32303
  Nonbonded interactions: 82016
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  90 "
            pdb=" HG1 THR A  93 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" H   VAL A 302 "
            pdb=" OE1 GLU A 308 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" O   SER A 145 "
            pdb=" H   ALA A 223 "
     model   vdw
     1.784 2.450
  nonbonded pdb=" OD1 ASP A  65 "
            pdb=" H   ARG A  66 "
     model   vdw
     1.790 2.450
  nonbonded pdb=" O   PRO A  81 "
            pdb="HE21 GLN A  86 "
     model   vdw
     1.791 2.450
  ... (remaining 82011 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=0.00 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:             3.130
  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:             0.100
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.140
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:11.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6199
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      :  0.002   0.027   2890  Z= 0.106
  Angle     :  0.486   3.747   3930  Z= 0.274
  Chirality :  0.039   0.128    426
  Planarity :  0.004   0.039    511
  Dihedral  : 11.962  85.429   1059
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.71 (0.45), residues: 363
  helix:  0.36 (0.40), residues: 169
  sheet:  0.78 (0.95), residues: 23
  loop :  0.79 (0.52), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 129 
 HIS   0.001   0.001   HIS A 203 
 PHE   0.005   0.001   PHE A  92 
 TYR   0.005   0.001   TYR A 283 
 ARG   0.001   0.000   ARG A 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16819 (  135)
  hydrogen bonds       : angle       7.49337 (  419)
  covalent geometry    : bond        0.00201 ( 2890)
  covalent geometry    : angle       0.48629 ( 3930)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 1.8553
  time to fit residues: 96.0418
Evaluate side-chains
  36 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.4592 r_free = 0.4592 target = 0.233107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.221743 restraints weight = 13297.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.4491 rms_B_bonded: 1.81
r_work: 0.4424 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.4344 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.4344
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4343
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4343 r_free = 0.4343    target_work(ls_wunit_k1) = 0.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4342 r_free = 0.4342    target_work(ls_wunit_k1) = 0.205         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4342
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6526
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   2890  Z= 0.229
  Angle     :  0.636   4.731   3930  Z= 0.350
  Chirality :  0.044   0.147    426
  Planarity :  0.005   0.038    511
  Dihedral  :  4.542  21.261    387
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  9.93 %
    Favored  : 89.73 %
  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:  0.09 (0.43), residues: 363
  helix: -0.08 (0.36), residues: 176
  sheet:  0.44 (1.01), residues: 23
  loop :  0.40 (0.52), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 340 
 HIS   0.004   0.001   HIS A  64 
 PHE   0.012   0.002   PHE A  47 
 TYR   0.015   0.002   TYR A 167 
 ARG   0.005   0.001   ARG A 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05493 (  135)
  hydrogen bonds       : angle       5.81597 (  419)
  covalent geometry    : bond        0.00497 ( 2890)
  covalent geometry    : angle       0.63553 ( 3930)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.5990 (tp) cc_final: 0.5679 (mt)
REVERT: A  144 LYS cc_start: 0.6999 (mmtt) cc_final: 0.6584 (mmpt)
REVERT: A  178 ILE cc_start: 0.5895 (pt) cc_final: 0.5629 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 49
  average time/residue: 1.9443
  time to fit residues: 98.4184
Evaluate side-chains
  40 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 33 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4628 r_free = 0.4628 target = 0.233859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.221246 restraints weight = 17436.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.4489 rms_B_bonded: 2.22
r_work: 0.4415 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work (final): 0.4415
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4416
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4416 r_free = 0.4416    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4416 r_free = 0.4416    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4416
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6471
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2890  Z= 0.144
  Angle     :  0.526   4.063   3930  Z= 0.279
  Chirality :  0.041   0.135    426
  Planarity :  0.004   0.034    511
  Dihedral  :  4.280  15.690    387
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 11.30 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.30 (0.44), residues: 363
  helix:  0.05 (0.37), residues: 177
  sheet:  0.84 (1.06), residues: 23
  loop :  0.53 (0.53), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 129 
 HIS   0.003   0.001   HIS A  64 
 PHE   0.010   0.001   PHE A  47 
 TYR   0.013   0.001   TYR A  99 
 ARG   0.003   0.001   ARG A 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05039 (  135)
  hydrogen bonds       : angle       5.45367 (  419)
  covalent geometry    : bond        0.00313 ( 2890)
  covalent geometry    : angle       0.52559 ( 3930)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.5979 (tp) cc_final: 0.5712 (mt)
REVERT: A  140 LYS cc_start: 0.6271 (mmtp) cc_final: 0.5869 (mmmt)
REVERT: A  144 LYS cc_start: 0.6938 (mmtt) cc_final: 0.6420 (mmpt)
REVERT: A  205 ASN cc_start: 0.7715 (m-40) cc_final: 0.7432 (m-40)
REVERT: A  316 ARG cc_start: 0.7729 (mtm180) cc_final: 0.7431 (mtm180)
  outliers start: 3
  outliers final: 2
  residues processed: 44
  average time/residue: 2.0248
  time to fit residues: 92.0531
Evaluate side-chains
  42 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   49 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4606 r_free = 0.4606 target = 0.231638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.219436 restraints weight = 17222.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.4475 rms_B_bonded: 2.16
r_work: 0.4399 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work (final): 0.4399
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4405
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4405 r_free = 0.4405    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4405 r_free = 0.4405    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4405
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6519
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2890  Z= 0.159
  Angle     :  0.545   4.645   3930  Z= 0.290
  Chirality :  0.041   0.134    426
  Planarity :  0.004   0.034    511
  Dihedral  :  4.349  18.115    387
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 11.64 %
    Favored  : 87.33 %
  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:  0.24 (0.44), residues: 363
  helix:  0.10 (0.38), residues: 177
  sheet:  0.46 (1.02), residues: 23
  loop :  0.43 (0.52), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 129 
 HIS   0.003   0.001   HIS A  64 
 PHE   0.009   0.001   PHE A  47 
 TYR   0.007   0.001   TYR A 167 
 ARG   0.003   0.001   ARG A 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04578 (  135)
  hydrogen bonds       : angle       5.41449 (  419)
  covalent geometry    : bond        0.00352 ( 2890)
  covalent geometry    : angle       0.54477 ( 3930)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.5909 (tp) cc_final: 0.5623 (mp)
REVERT: A  140 LYS cc_start: 0.6255 (mmtp) cc_final: 0.5828 (mmmt)
REVERT: A  144 LYS cc_start: 0.6911 (mmtt) cc_final: 0.6455 (mmpt)
REVERT: A  205 ASN cc_start: 0.7749 (m-40) cc_final: 0.7477 (m-40)
REVERT: A  328 GLU cc_start: 0.7567 (tt0) cc_final: 0.7197 (pt0)
  outliers start: 3
  outliers final: 2
  residues processed: 46
  average time/residue: 1.8677
  time to fit residues: 89.0433
Evaluate side-chains
  43 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   49 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.4591 r_free = 0.4591 target = 0.229946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.218763 restraints weight = 14560.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.4466 rms_B_bonded: 1.93
r_work: 0.4396 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.4311 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.4311
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4317
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4317 r_free = 0.4317    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4317 r_free = 0.4317    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4317
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2890  Z= 0.158
  Angle     :  0.533   4.568   3930  Z= 0.282
  Chirality :  0.041   0.135    426
  Planarity :  0.004   0.033    511
  Dihedral  :  4.358  17.451    387
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 11.30 %
    Favored  : 87.33 %
  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:  0.12 (0.44), residues: 363
  helix:  0.09 (0.38), residues: 177
  sheet:  0.39 (0.99), residues: 23
  loop :  0.24 (0.51), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 129 
 HIS   0.002   0.001   HIS A  64 
 PHE   0.010   0.001   PHE A  47 
 TYR   0.006   0.001   TYR A  99 
 ARG   0.002   0.001   ARG A 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04594 (  135)
  hydrogen bonds       : angle       5.35740 (  419)
  covalent geometry    : bond        0.00351 ( 2890)
  covalent geometry    : angle       0.53261 ( 3930)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.6029 (tp) cc_final: 0.5657 (mp)
REVERT: A  140 LYS cc_start: 0.6381 (mmtp) cc_final: 0.5974 (mmmt)
REVERT: A  144 LYS cc_start: 0.7148 (mmtt) cc_final: 0.6669 (mmpt)
REVERT: A  205 ASN cc_start: 0.7856 (m-40) cc_final: 0.7609 (m-40)
REVERT: A  328 GLU cc_start: 0.7775 (tt0) cc_final: 0.7432 (pt0)
REVERT: A  365 GLN cc_start: 0.6683 (tp-100) cc_final: 0.6145 (tt0)
  outliers start: 4
  outliers final: 3
  residues processed: 47
  average time/residue: 1.8167
  time to fit residues: 88.6218
Evaluate side-chains
  44 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain A residue   73 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0980
   chunk 3 optimal weight:    0.0170
   chunk 16 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.230823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.219228 restraints weight = 16072.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.4469 rms_B_bonded: 2.12
r_work: 0.4396 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.4306 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4305 r_free = 0.4305    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4305 r_free = 0.4305    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6621
moved from start:          0.3904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2890  Z= 0.118
  Angle     :  0.512   4.639   3930  Z= 0.263
  Chirality :  0.040   0.133    426
  Planarity :  0.004   0.033    511
  Dihedral  :  4.102  14.876    387
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 10.96 %
    Favored  : 86.64 %
  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:  0.35 (0.44), residues: 363
  helix:  0.24 (0.38), residues: 177
  sheet:  0.56 (0.97), residues: 23
  loop :  0.41 (0.52), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 129 
 HIS   0.002   0.001   HIS A  39 
 PHE   0.006   0.001   PHE A  92 
 TYR   0.008   0.001   TYR A  99 
 ARG   0.002   0.001   ARG A 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03989 (  135)
  hydrogen bonds       : angle       5.17603 (  419)
  covalent geometry    : bond        0.00258 ( 2890)
  covalent geometry    : angle       0.51202 ( 3930)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.6000 (tp) cc_final: 0.5643 (mp)
REVERT: A  140 LYS cc_start: 0.6345 (mmtp) cc_final: 0.5962 (mmmt)
REVERT: A  144 LYS cc_start: 0.7108 (mmtt) cc_final: 0.6606 (mmpt)
REVERT: A  205 ASN cc_start: 0.7848 (m-40) cc_final: 0.7618 (m-40)
REVERT: A  328 GLU cc_start: 0.7850 (tt0) cc_final: 0.7481 (pt0)
  outliers start: 6
  outliers final: 3
  residues processed: 46
  average time/residue: 1.7385
  time to fit residues: 83.1644
Evaluate side-chains
  44 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain A residue   73 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 25 optimal weight:    0.3980
   chunk 5 optimal weight:    0.0970
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 20 optimal weight:    0.3980
   chunk 24 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.4178

-------------------------------------------------------------------------------
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 = 0.4604 r_free = 0.4604 target = 0.231280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.218912 restraints weight = 18659.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.4466 rms_B_bonded: 2.34
r_work: 0.4387 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.4387
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4396
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4396 r_free = 0.4396    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4396 r_free = 0.4396    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6524
moved from start:          0.4055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2890  Z= 0.114
  Angle     :  0.501   4.516   3930  Z= 0.256
  Chirality :  0.040   0.136    426
  Planarity :  0.004   0.032    511
  Dihedral  :  4.020  14.800    387
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.33 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.40 (0.44), residues: 363
  helix:  0.29 (0.38), residues: 174
  sheet:  0.64 (0.97), residues: 23
  loop :  0.41 (0.51), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 129 
 HIS   0.001   0.000   HIS A  64 
 PHE   0.009   0.001   PHE A 217 
 TYR   0.007   0.001   TYR A  99 
 ARG   0.001   0.000   ARG A 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03894 (  135)
  hydrogen bonds       : angle       5.08262 (  419)
  covalent geometry    : bond        0.00252 ( 2890)
  covalent geometry    : angle       0.50138 ( 3930)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.5968 (tp) cc_final: 0.5648 (mp)
REVERT: A  140 LYS cc_start: 0.6130 (mmtp) cc_final: 0.5765 (mmmt)
REVERT: A  144 LYS cc_start: 0.6966 (mmtt) cc_final: 0.6459 (mmpt)
REVERT: A  205 ASN cc_start: 0.7749 (m-40) cc_final: 0.7539 (m-40)
REVERT: A  328 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7400 (pt0)
  outliers start: 5
  outliers final: 3
  residues processed: 44
  average time/residue: 1.7392
  time to fit residues: 79.6716
Evaluate side-chains
  44 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  328 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    0.0970
   chunk 2 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0980
   chunk 27 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.4178

-------------------------------------------------------------------------------
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 = 0.4602 r_free = 0.4602 target = 0.231052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.219256 restraints weight = 16974.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.4464 rms_B_bonded: 2.19
r_work: 0.4392 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.4301 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4302
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4302 r_free = 0.4302    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4302 r_free = 0.4302    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4302
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6624
moved from start:          0.4134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2890  Z= 0.110
  Angle     :  0.502   4.482   3930  Z= 0.255
  Chirality :  0.040   0.132    426
  Planarity :  0.004   0.031    511
  Dihedral  :  3.954  14.535    387
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.33 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.50 (0.44), residues: 363
  helix:  0.34 (0.38), residues: 174
  sheet:  0.74 (0.98), residues: 23
  loop :  0.49 (0.52), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 129 
 HIS   0.001   0.001   HIS A  64 
 PHE   0.007   0.001   PHE A  47 
 TYR   0.006   0.001   TYR A  99 
 ARG   0.002   0.001   ARG A 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03776 (  135)
  hydrogen bonds       : angle       5.02785 (  419)
  covalent geometry    : bond        0.00246 ( 2890)
  covalent geometry    : angle       0.50163 ( 3930)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.6024 (tp) cc_final: 0.5678 (mp)
REVERT: A  140 LYS cc_start: 0.6364 (mmtp) cc_final: 0.6018 (mmmt)
REVERT: A  144 LYS cc_start: 0.7131 (mmtt) cc_final: 0.6620 (mmpt)
REVERT: A  178 ILE cc_start: 0.7356 (mm) cc_final: 0.7025 (mp)
REVERT: A  205 ASN cc_start: 0.7792 (m-40) cc_final: 0.7584 (m-40)
REVERT: A  328 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7539 (pt0)
  outliers start: 5
  outliers final: 3
  residues processed: 45
  average time/residue: 1.5585
  time to fit residues: 73.2420
Evaluate side-chains
  42 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  328 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0570
   chunk 2 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    0.2980
   chunk 21 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 29 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.3898

-------------------------------------------------------------------------------
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 = 0.4601 r_free = 0.4601 target = 0.230971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.219052 restraints weight = 17427.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.4461 rms_B_bonded: 2.22
r_work: 0.4389 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work (final): 0.4389
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4396
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4396 r_free = 0.4396    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4396 r_free = 0.4396    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6513
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2890  Z= 0.108
  Angle     :  0.490   4.416   3930  Z= 0.250
  Chirality :  0.040   0.130    426
  Planarity :  0.004   0.031    511
  Dihedral  :  3.906  13.773    387
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.67 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.54 (0.44), residues: 363
  helix:  0.38 (0.38), residues: 174
  sheet:  0.79 (0.97), residues: 23
  loop :  0.50 (0.52), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 340 
 HIS   0.001   0.000   HIS A  64 
 PHE   0.007   0.001   PHE A 217 
 TYR   0.008   0.001   TYR A 171 
 ARG   0.002   0.000   ARG A 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  135)
  hydrogen bonds       : angle       4.99035 (  419)
  covalent geometry    : bond        0.00241 ( 2890)
  covalent geometry    : angle       0.49024 ( 3930)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.5972 (tp) cc_final: 0.5686 (mp)
REVERT: A  140 LYS cc_start: 0.6112 (mmtp) cc_final: 0.5761 (mmmt)
REVERT: A  144 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6448 (mmpt)
REVERT: A  178 ILE cc_start: 0.7322 (mm) cc_final: 0.6991 (mp)
REVERT: A  205 ASN cc_start: 0.7754 (m-40) cc_final: 0.7541 (m-40)
  outliers start: 4
  outliers final: 3
  residues processed: 39
  average time/residue: 1.7818
  time to fit residues: 72.4427
Evaluate side-chains
  39 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain A residue   73 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 15 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 3 optimal weight:    0.0270
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.4238

-------------------------------------------------------------------------------
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 = 0.4601 r_free = 0.4601 target = 0.231036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.219003 restraints weight = 17790.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.4461 rms_B_bonded: 2.27
r_work: 0.4388 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work (final): 0.4388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4399 r_free = 0.4399    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4399 r_free = 0.4399    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6524
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2890  Z= 0.110
  Angle     :  0.495   4.420   3930  Z= 0.252
  Chirality :  0.040   0.130    426
  Planarity :  0.004   0.031    511
  Dihedral  :  3.912  14.170    387
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.67 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.51 (0.44), residues: 363
  helix:  0.37 (0.38), residues: 174
  sheet:  0.74 (0.97), residues: 23
  loop :  0.47 (0.52), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 340 
 HIS   0.001   0.001   HIS A  64 
 PHE   0.007   0.001   PHE A 217 
 TYR   0.009   0.001   TYR A 171 
 ARG   0.001   0.000   ARG A 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  135)
  hydrogen bonds       : angle       4.99122 (  419)
  covalent geometry    : bond        0.00248 ( 2890)
  covalent geometry    : angle       0.49454 ( 3930)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.5982 (tp) cc_final: 0.5709 (mp)
REVERT: A  140 LYS cc_start: 0.6155 (mmtp) cc_final: 0.5807 (mmmt)
REVERT: A  144 LYS cc_start: 0.6978 (mmtt) cc_final: 0.6482 (mmpt)
REVERT: A  178 ILE cc_start: 0.7350 (mm) cc_final: 0.7036 (mp)
REVERT: A  365 GLN cc_start: 0.6403 (tp-100) cc_final: 0.5880 (tt0)
  outliers start: 4
  outliers final: 3
  residues processed: 41
  average time/residue: 1.8455
  time to fit residues: 79.0879
Evaluate side-chains
  41 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain A residue   73 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0980
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.229903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.219097 restraints weight = 13433.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.4466 rms_B_bonded: 1.88
r_work: 0.4404 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.4319 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4324
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4324 r_free = 0.4324    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4324 r_free = 0.4324    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4324
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6629
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2890  Z= 0.128
  Angle     :  0.507   4.419   3930  Z= 0.261
  Chirality :  0.041   0.129    426
  Planarity :  0.004   0.031    511
  Dihedral  :  4.008  15.137    387
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.67 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.39 (0.44), residues: 363
  helix:  0.29 (0.38), residues: 174
  sheet:  0.55 (0.95), residues: 23
  loop :  0.40 (0.51), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 340 
 HIS   0.001   0.001   HIS A  64 
 PHE   0.009   0.001   PHE A  47 
 TYR   0.010   0.001   TYR A 171 
 ARG   0.001   0.000   ARG A 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  135)
  hydrogen bonds       : angle       5.10801 (  419)
  covalent geometry    : bond        0.00288 ( 2890)
  covalent geometry    : angle       0.50708 ( 3930)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5879.96 seconds
wall clock time: 102 minutes 42.99 seconds (6162.99 seconds total)