Starting phenix.real_space_refine
on Sat Apr 26 21:41:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qt6_18644/04_2025/8qt6_18644.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qt6_18644/04_2025/8qt6_18644.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qt6_18644/04_2025/8qt6_18644.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qt6_18644/04_2025/8qt6_18644.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qt6_18644/04_2025/8qt6_18644.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qt6_18644/04_2025/8qt6_18644.cif"
  }
  resolution = 2.29
  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=   0.101
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: 6
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     P       2      5.49       5
     S      11      5.16       5
     C    2261      2.51       5
     N     548      2.21       5
     O     642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3466
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3264
          Classifications: {'peptide': 399}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 385}
    Chain: "A"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 202
          Unusual residues: {'FAD': 1, 'HEM': 2}
          Classifications: {'undetermined': 3, 'water': 63}
          Link IDs: {None: 65}
  Time building chain proxies: 3.16, per 1000 atoms: 0.91
  Number of scatterers: 3466
  At special positions: 0
  Unit cell: (62.1736, 67.1876, 92.2576, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      2     26.01
     S      11     16.00
     P       2     15.00
     O     642      8.00
     N     548      7.00
     C    2261      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.28
  Conformation dependent library (CDL) restraints added in 421.9 milliseconds
  

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  740

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 2 sheets defined
      56.1% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 6
      No H-bonds generated for 'chain 'A' and resid 4 through 6'
    Processing helix  chain 'A' and resid 7 through 29
    Processing helix  chain 'A' and resid 32 through 48
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 61 through 88
    Processing helix  chain 'A' and resid 94 through 115
      removed outlier: 3.570A  pdb=" N   GLY A 100 " --> pdb=" O   ALA A  96 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TYR A 115 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 130
    Processing helix  chain 'A' and resid 131 through 148
    Processing helix  chain 'A' and resid 149 through 152
    Processing helix  chain 'A' and resid 155 through 178
    Processing helix  chain 'A' and resid 178 through 183
    Processing helix  chain 'A' and resid 253 through 263
      removed outlier: 3.642A  pdb=" N   LEU A 263 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 296 through 306
    Processing helix  chain 'A' and resid 321 through 325
    Processing helix  chain 'A' and resid 327 through 338
    Processing helix  chain 'A' and resid 372 through 387
      removed outlier: 3.921A  pdb=" N   ALA A 378 " --> pdb=" O   SER A 374 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 379 " --> pdb=" O   MET A 375 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 236
      removed outlier: 3.708A  pdb=" N   LYS A 268 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   ILE A 190 " --> pdb=" O   HIS A 206 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   HIS A 206 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   HIS A 192 " --> pdb=" O   GLN A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 347
      removed outlier: 6.865A  pdb=" N   GLN A 287 " --> pdb=" O   HIS A 314 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   TYR A 316 " --> pdb=" O   GLN A 287 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   TRP A 289 " --> pdb=" O   TYR A 316 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   SER A 318 " --> pdb=" O   TRP A 289 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ALA A 291 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ALA A 365 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   ILE A 393 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   VAL A 367 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   GLU A 395 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   MET A 369 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)

    187 hydrogen bonds defined for protein.
    540 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: 1.15

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.23 -     1.39: 1504
        1.39 -     1.56: 1981
        1.56 -     1.73: 4
        1.73 -     1.89: 21
        1.89 -     2.06: 8
  Bond restraints: 3518
  Sorted by residual:
  bond pdb=" O3P FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.588  0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" O5B FAD A 501 "
       pdb=" PA  FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.563  0.071 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" O5' FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.637  1.572  0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" O3P FAD A 501 "
       pdb=" PA  FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.633  1.586  0.047 2.00e-02 2.50e+03 5.51e+00
  bond pdb=" O1P FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.492  1.531 -0.039 2.00e-02 2.50e+03 3.75e+00
  ... (remaining 3513 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 4683
        1.44 -     2.89: 75
        2.89 -     4.33: 27
        4.33 -     5.78: 13
        5.78 -     7.22: 3
  Bond angle restraints: 4801
  Sorted by residual:
  angle pdb=" O1P FAD A 501 "
        pdb=" P   FAD A 501 "
        pdb=" O2P FAD A 501 "
      ideal   model   delta    sigma   weight residual
     122.50  115.28    7.22 3.00e+00 1.11e-01 5.79e+00
  angle pdb=" O1A FAD A 501 "
        pdb=" PA  FAD A 501 "
        pdb=" O5B FAD A 501 "
      ideal   model   delta    sigma   weight residual
     104.10  110.80   -6.70 3.00e+00 1.11e-01 4.98e+00
  angle pdb=" CA  LEU A 187 "
        pdb=" CB  LEU A 187 "
        pdb=" CG  LEU A 187 "
      ideal   model   delta    sigma   weight residual
     116.30  123.09   -6.79 3.50e+00 8.16e-02 3.76e+00
  angle pdb=" C3B HEM A 503 "
        pdb=" CAB HEM A 503 "
        pdb=" CBB HEM A 503 "
      ideal   model   delta    sigma   weight residual
     120.00  125.65   -5.65 3.00e+00 1.11e-01 3.55e+00
  angle pdb=" CA  TYR A 275 "
        pdb=" CB  TYR A 275 "
        pdb=" CG  TYR A 275 "
      ideal   model   delta    sigma   weight residual
     113.90  117.28   -3.38 1.80e+00 3.09e-01 3.54e+00
  ... (remaining 4796 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 1709
       17.72 -    35.45: 201
       35.45 -    53.17: 65
       53.17 -    70.89: 16
       70.89 -    88.62: 11
  Dihedral angle restraints: 2002
    sinusoidal: 840
      harmonic: 1162
  Sorted by residual:
  dihedral pdb=" C2D HEM A 503 "
           pdb=" C3D HEM A 503 "
           pdb=" CAD HEM A 503 "
           pdb=" CBD HEM A 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   75.35  -75.35     2      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" C1A HEM A 503 "
           pdb=" C2A HEM A 503 "
           pdb=" CAA HEM A 503 "
           pdb=" CBA HEM A 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   71.87  -71.87     2      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" C1A HEM A 502 "
           pdb=" C2A HEM A 502 "
           pdb=" CAA HEM A 502 "
           pdb=" CBA HEM A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -71.84   71.84     2      2.00e+01 2.50e-03 1.08e+01
  ... (remaining 1999 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 299
       0.028 -    0.056: 124
       0.056 -    0.085: 47
       0.085 -    0.113: 24
       0.113 -    0.141: 7
  Chirality restraints: 501
  Sorted by residual:
  chirality pdb=" C2B FAD A 501 "
            pdb=" C1B FAD A 501 "
            pdb=" C3B FAD A 501 "
            pdb=" O2B FAD A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.68    0.14 2.00e-01 2.50e+01 4.98e-01
  chirality pdb=" CA  ILE A 203 "
            pdb=" N   ILE A 203 "
            pdb=" C   ILE A 203 "
            pdb=" CB  ILE A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  THR A 297 "
            pdb=" N   THR A 297 "
            pdb=" C   THR A 297 "
            pdb=" CB  THR A 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 498 not shown)

  Planarity restraints: 576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 361 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO A 362 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 362 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 362 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A  43 "    0.007 2.00e-02 2.50e+03   1.35e-02 1.82e+00
        pdb=" C   SER A  43 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   SER A  43 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU A  44 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A  41 "   -0.006 2.00e-02 2.50e+03   1.28e-02 1.65e+00
        pdb=" C   SER A  41 "    0.022 2.00e-02 2.50e+03
        pdb=" O   SER A  41 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LEU A  42 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 573 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 137
        2.72 -     3.26: 3332
        3.26 -     3.81: 6257
        3.81 -     4.35: 8020
        4.35 -     4.90: 12844
  Nonbonded interactions: 30590
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A 129 "
            pdb="FE   HEM A 503 "
     model   vdw
     2.174 3.080
  nonbonded pdb=" O1P FAD A 501 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   HOH A 601 "
            pdb=" O   HOH A 633 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   HOH A 606 "
            pdb=" O   HOH A 661 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   HOH A 612 "
            pdb=" O   HOH A 620 "
     model   vdw
     2.257 3.040
  ... (remaining 30585 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:             1.940
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.280
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:14.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
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      :  0.005   0.106   3520  Z= 0.189
  Angle     :  0.596   7.222   4801  Z= 0.275
  Chirality :  0.040   0.141    501
  Planarity :  0.004   0.043    576
  Dihedral  : 18.307  88.618   1262
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 19.02 %
    Favored  : 80.12 %
  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:  0.77 (0.44), residues: 397
  helix:  0.95 (0.37), residues: 198
  sheet:  0.34 (0.54), residues: 89
  loop :  0.13 (0.68), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A  69 
 PHE   0.009   0.001   PHE A  82 
 TYR   0.014   0.001   TYR A 275 
 ARG   0.001   0.000   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13302 (  187)
  hydrogen bonds       : angle       6.85087 (  540)
  covalent geometry    : bond        0.00411 ( 3518)
  covalent geometry    : angle       0.59637 ( 4801)
  Misc. bond           : bond        0.08250 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  186 TYR cc_start: 0.8912 (m-80) cc_final: 0.8572 (m-80)
REVERT: A  385 LYS cc_start: 0.6845 (tttt) cc_final: 0.6543 (ttmp)
  outliers start: 3
  outliers final: 3
  residues processed: 47
  average time/residue: 0.9085
  time to fit residues: 44.6988
Evaluate side-chains
  46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 SER
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  328 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 121 GLN
A 149 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.122783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.101535 restraints weight = 3347.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 1.23
r_work: 0.3047 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.0852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.253   3520  Z= 0.171
  Angle     :  0.682  14.892   4801  Z= 0.296
  Chirality :  0.042   0.147    501
  Planarity :  0.004   0.043    576
  Dihedral  : 11.219  88.185    504
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.00 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.50 (0.43), residues: 397
  helix:  1.87 (0.36), residues: 201
  sheet:  0.24 (0.54), residues: 88
  loop :  0.13 (0.64), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  25 
 HIS   0.008   0.001   HIS A  69 
 PHE   0.011   0.001   PHE A  82 
 TYR   0.015   0.002   TYR A 144 
 ARG   0.001   0.000   ARG A  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04379 (  187)
  hydrogen bonds       : angle       4.84413 (  540)
  covalent geometry    : bond        0.00404 ( 3518)
  covalent geometry    : angle       0.68203 ( 4801)
  Misc. bond           : bond        0.20243 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7859 (tp30)
REVERT: A  320 ARG cc_start: 0.7414 (mtp85) cc_final: 0.7062 (mtp85)
REVERT: A  385 LYS cc_start: 0.6938 (tttt) cc_final: 0.6549 (ttmp)
  outliers start: 7
  outliers final: 2
  residues processed: 51
  average time/residue: 1.0544
  time to fit residues: 55.8389
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  121 GLN
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3400 r_free = 0.3400 target = 0.122619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.101349 restraints weight = 3331.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.24
r_work: 0.3044 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.0861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.230   3520  Z= 0.171
  Angle     :  0.662  14.508   4801  Z= 0.291
  Chirality :  0.042   0.145    501
  Planarity :  0.003   0.041    576
  Dihedral  : 11.078  83.337    499
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.85 %
    Favored  : 81.84 %
  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:  1.35 (0.42), residues: 397
  helix:  1.76 (0.36), residues: 202
  sheet:  0.19 (0.53), residues: 88
  loop : -0.01 (0.61), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A  69 
 PHE   0.010   0.001   PHE A  82 
 TYR   0.015   0.002   TYR A 275 
 ARG   0.001   0.000   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04280 (  187)
  hydrogen bonds       : angle       4.78058 (  540)
  covalent geometry    : bond        0.00406 ( 3518)
  covalent geometry    : angle       0.66242 ( 4801)
  Misc. bond           : bond        0.18530 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7695 (mp)
REVERT: A  285 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7750 (tp30)
REVERT: A  320 ARG cc_start: 0.7321 (mtp85) cc_final: 0.6947 (mtp85)
  outliers start: 8
  outliers final: 2
  residues processed: 52
  average time/residue: 1.0701
  time to fit residues: 57.7335
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  375 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 30 optimal weight:    0.2980
   chunk 21 optimal weight:    0.6980
   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 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.123942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.102524 restraints weight = 3351.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.29
r_work: 0.3059 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.0898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.183   3520  Z= 0.119
  Angle     :  0.593  13.599   4801  Z= 0.259
  Chirality :  0.040   0.142    501
  Planarity :  0.003   0.040    576
  Dihedral  : 10.015  80.953    499
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.87 %
    Favored  : 80.40 %
  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:  1.55 (0.42), residues: 397
  helix:  1.99 (0.36), residues: 202
  sheet:  0.16 (0.54), residues: 88
  loop :  0.08 (0.62), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A  69 
 PHE   0.009   0.001   PHE A 218 
 TYR   0.014   0.001   TYR A 275 
 ARG   0.000   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (  187)
  hydrogen bonds       : angle       4.52682 (  540)
  covalent geometry    : bond        0.00286 ( 3518)
  covalent geometry    : angle       0.59336 ( 4801)
  Misc. bond           : bond        0.15465 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7613 (mp)
REVERT: A  272 ASP cc_start: 0.8769 (p0) cc_final: 0.8530 (p0)
  outliers start: 6
  outliers final: 1
  residues processed: 48
  average time/residue: 0.8756
  time to fit residues: 44.0977
Evaluate side-chains
  47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  375 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0370
   overall best weight:    0.9462

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.122788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.101168 restraints weight = 3417.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.32
r_work: 0.3040 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.0926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.194   3520  Z= 0.142
  Angle     :  0.626  14.168   4801  Z= 0.274
  Chirality :  0.041   0.143    501
  Planarity :  0.003   0.041    576
  Dihedral  : 10.392  78.469    499
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.87 %
    Favored  : 80.40 %
  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:  1.42 (0.42), residues: 397
  helix:  1.86 (0.36), residues: 202
  sheet:  0.14 (0.54), residues: 88
  loop :  0.03 (0.61), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A  69 
 PHE   0.011   0.001   PHE A  82 
 TYR   0.015   0.002   TYR A 275 
 ARG   0.001   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03861 (  187)
  hydrogen bonds       : angle       4.61288 (  540)
  covalent geometry    : bond        0.00342 ( 3518)
  covalent geometry    : angle       0.62586 ( 4801)
  Misc. bond           : bond        0.16000 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7518 (mp)
REVERT: A  272 ASP cc_start: 0.8777 (p0) cc_final: 0.8522 (p0)
REVERT: A  285 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7709 (tp30)
  outliers start: 6
  outliers final: 1
  residues processed: 48
  average time/residue: 0.9352
  time to fit residues: 46.7862
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  375 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.123428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.101829 restraints weight = 3407.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 1.31
r_work: 0.3048 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.0925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.184   3520  Z= 0.133
  Angle     :  0.615  13.733   4801  Z= 0.270
  Chirality :  0.040   0.142    501
  Planarity :  0.003   0.041    576
  Dihedral  : 10.168  79.154    499
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.87 %
    Favored  : 80.12 %
  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:  1.45 (0.42), residues: 397
  helix:  1.89 (0.36), residues: 202
  sheet:  0.14 (0.54), residues: 88
  loop :  0.05 (0.61), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A  69 
 PHE   0.010   0.001   PHE A  82 
 TYR   0.015   0.002   TYR A 275 
 ARG   0.001   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03712 (  187)
  hydrogen bonds       : angle       4.56810 (  540)
  covalent geometry    : bond        0.00321 ( 3518)
  covalent geometry    : angle       0.61453 ( 4801)
  Misc. bond           : bond        0.15246 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7609 (mp)
REVERT: A  272 ASP cc_start: 0.8765 (p0) cc_final: 0.8513 (p0)
REVERT: A  285 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7722 (tp30)
  outliers start: 7
  outliers final: 1
  residues processed: 51
  average time/residue: 0.9873
  time to fit residues: 52.5040
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  375 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   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 = 0.3411 r_free = 0.3411 target = 0.123979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.102372 restraints weight = 3356.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.30
r_work: 0.3058 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.0942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.183   3520  Z= 0.124
  Angle     :  0.603  13.516   4801  Z= 0.265
  Chirality :  0.040   0.140    501
  Planarity :  0.003   0.040    576
  Dihedral  :  9.910  79.599    499
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.73 %
    Favored  : 79.54 %
  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:  1.48 (0.42), residues: 397
  helix:  1.93 (0.36), residues: 202
  sheet:  0.13 (0.54), residues: 88
  loop :  0.05 (0.62), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A  69 
 PHE   0.010   0.001   PHE A  85 
 TYR   0.014   0.001   TYR A 275 
 ARG   0.000   0.000   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03570 (  187)
  hydrogen bonds       : angle       4.50596 (  540)
  covalent geometry    : bond        0.00298 ( 3518)
  covalent geometry    : angle       0.60324 ( 4801)
  Misc. bond           : bond        0.15107 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7595 (mp)
REVERT: A  272 ASP cc_start: 0.8762 (p0) cc_final: 0.8520 (p0)
REVERT: A  285 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7716 (tp30)
  outliers start: 6
  outliers final: 1
  residues processed: 51
  average time/residue: 1.1191
  time to fit residues: 59.2394
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0070
   chunk 25 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0470
   chunk 24 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
A 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.126648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.105466 restraints weight = 3396.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.27
r_work: 0.3097 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.150   3520  Z= 0.099
  Angle     :  0.563  12.290   4801  Z= 0.247
  Chirality :  0.039   0.138    501
  Planarity :  0.003   0.040    576
  Dihedral  :  9.214  81.759    499
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 19.31 %
    Favored  : 79.54 %
  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:  1.66 (0.43), residues: 397
  helix:  2.10 (0.36), residues: 202
  sheet:  0.15 (0.54), residues: 88
  loop :  0.13 (0.62), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  25 
 HIS   0.005   0.001   HIS A  69 
 PHE   0.009   0.001   PHE A  85 
 TYR   0.013   0.001   TYR A 275 
 ARG   0.001   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03080 (  187)
  hydrogen bonds       : angle       4.31119 (  540)
  covalent geometry    : bond        0.00245 ( 3518)
  covalent geometry    : angle       0.56343 ( 4801)
  Misc. bond           : bond        0.12379 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7622 (mp)
REVERT: A  149 ASN cc_start: 0.7941 (m-40) cc_final: 0.7099 (t0)
REVERT: A  272 ASP cc_start: 0.8732 (p0) cc_final: 0.8492 (p0)
REVERT: A  285 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7740 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 52
  average time/residue: 1.0300
  time to fit residues: 55.8863
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 33 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0030
   chunk 19 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
A 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.126992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.104725 restraints weight = 3319.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.46
r_work: 0.3103 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.154   3520  Z= 0.105
  Angle     :  0.578  12.776   4801  Z= 0.252
  Chirality :  0.039   0.138    501
  Planarity :  0.003   0.040    576
  Dihedral  :  9.290  80.205    499
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 19.60 %
    Favored  : 79.83 %
  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:  1.68 (0.43), residues: 397
  helix:  2.11 (0.36), residues: 202
  sheet:  0.15 (0.54), residues: 88
  loop :  0.17 (0.62), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A  69 
 PHE   0.011   0.001   PHE A  85 
 TYR   0.013   0.001   TYR A 275 
 ARG   0.001   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03204 (  187)
  hydrogen bonds       : angle       4.31360 (  540)
  covalent geometry    : bond        0.00258 ( 3518)
  covalent geometry    : angle       0.57763 ( 4801)
  Misc. bond           : bond        0.12604 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7513 (mp)
REVERT: A  149 ASN cc_start: 0.7879 (m-40) cc_final: 0.7005 (t0)
REVERT: A  264 GLN cc_start: 0.7774 (mp-120) cc_final: 0.7452 (mp10)
REVERT: A  272 ASP cc_start: 0.8727 (p0) cc_final: 0.8492 (p0)
  outliers start: 2
  outliers final: 1
  residues processed: 48
  average time/residue: 0.7945
  time to fit residues: 40.0417
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  153 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0980
   chunk 9 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.125436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.102851 restraints weight = 3362.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.48
r_work: 0.3076 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.176   3520  Z= 0.124
  Angle     :  0.606  13.501   4801  Z= 0.266
  Chirality :  0.040   0.139    501
  Planarity :  0.003   0.040    576
  Dihedral  :  9.648  78.584    499
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 19.60 %
    Favored  : 79.54 %
  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:  1.58 (0.42), residues: 397
  helix:  2.00 (0.36), residues: 202
  sheet:  0.13 (0.54), residues: 88
  loop :  0.16 (0.62), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A  69 
 PHE   0.011   0.001   PHE A  85 
 TYR   0.015   0.002   TYR A 275 
 ARG   0.000   0.000   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03564 (  187)
  hydrogen bonds       : angle       4.45015 (  540)
  covalent geometry    : bond        0.00300 ( 3518)
  covalent geometry    : angle       0.60576 ( 4801)
  Misc. bond           : bond        0.14367 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7465 (mp)
REVERT: A  186 TYR cc_start: 0.8678 (m-80) cc_final: 0.8314 (m-80)
REVERT: A  272 ASP cc_start: 0.8746 (p0) cc_final: 0.8451 (p0)
REVERT: A  285 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7714 (tp30)
  outliers start: 3
  outliers final: 1
  residues processed: 48
  average time/residue: 0.8556
  time to fit residues: 43.0007
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0670
   chunk 0 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0370
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.126935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.104764 restraints weight = 3375.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 1.47
r_work: 0.3104 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.153   3520  Z= 0.103
  Angle     :  0.571  12.432   4801  Z= 0.250
  Chirality :  0.039   0.138    501
  Planarity :  0.003   0.040    576
  Dihedral  :  9.236  80.737    499
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 19.31 %
    Favored  : 79.83 %
  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:  1.70 (0.43), residues: 397
  helix:  2.12 (0.36), residues: 202
  sheet:  0.15 (0.54), residues: 88
  loop :  0.19 (0.62), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A  69 
 PHE   0.012   0.001   PHE A  85 
 TYR   0.013   0.001   TYR A 275 
 ARG   0.001   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03165 (  187)
  hydrogen bonds       : angle       4.31707 (  540)
  covalent geometry    : bond        0.00256 ( 3518)
  covalent geometry    : angle       0.57112 ( 4801)
  Misc. bond           : bond        0.12403 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3078.07 seconds
wall clock time: 53 minutes 22.48 seconds (3202.48 seconds total)