Starting phenix.real_space_refine
on Tue Feb  3 15:17:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nbm_49232/02_2026/9nbm_49232_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nbm_49232/02_2026/9nbm_49232.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nbm_49232/02_2026/9nbm_49232_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nbm_49232/02_2026/9nbm_49232_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nbm_49232/02_2026/9nbm_49232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nbm_49232/02_2026/9nbm_49232.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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
     P       4      5.49       5
     Mg      2      5.21       5
     S      12      5.16       5
     C    2646      2.51       5
     N     749      2.21       5
     O     807      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4220
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 552, 4164
          Classifications: {'peptide': 552}
          Link IDs: {'PTRANS': 32, 'TRANS': 519}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {' MG': 2, 'ADP': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 0.76, per 1000 atoms: 0.18
  Number of scatterers: 4220
  At special positions: 0
  Unit cell: (56.55, 80.6, 87.1, 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)
     S      12     16.00
     P       4     15.00
     Mg      2     11.99
     O     807      8.00
     N     749      7.00
     C    2646      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 290.7 milliseconds
  

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1030

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 5 sheets defined
      55.4% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 37
    Processing helix  chain 'A' and resid 50 through 56
    Processing helix  chain 'A' and resid 78 through 92
    Processing helix  chain 'A' and resid 99 through 110
    Processing helix  chain 'A' and resid 112 through 128
    Processing helix  chain 'A' and resid 132 through 137
      removed outlier: 3.840A  pdb=" N   TYR A 137 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 156
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 183 through 196
      removed outlier: 3.663A  pdb=" N   TYR A 187 " --> pdb=" O   GLN A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 227
    Processing helix  chain 'A' and resid 240 through 245
    Processing helix  chain 'A' and resid 247 through 263
    Processing helix  chain 'A' and resid 265 through 269
    Processing helix  chain 'A' and resid 285 through 291
      removed outlier: 3.604A  pdb=" N   GLN A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 325
      removed outlier: 4.170A  pdb=" N   LEU A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 354
    Processing helix  chain 'A' and resid 372 through 377
      removed outlier: 4.192A  pdb=" N   SER A 376 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 400
      removed outlier: 3.773A  pdb=" N   GLU A 400 " --> pdb=" O   GLN A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 418
    Processing helix  chain 'A' and resid 420 through 439
      removed outlier: 3.822A  pdb=" N   ARG A 434 " --> pdb=" O   GLN A 430 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ILE A 435 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 463
    Processing helix  chain 'A' and resid 482 through 488
      removed outlier: 3.750A  pdb=" N   LEU A 486 " --> pdb=" O   PRO A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 519
    Processing helix  chain 'A' and resid 538 through 559
    Processing helix  chain 'A' and resid 579 through 584
      removed outlier: 3.749A  pdb=" N   ILE A 583 " --> pdb=" O   LEU A 579 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12
      removed outlier: 6.780A  pdb=" N   MET A  12 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15
      removed outlier: 6.005A  pdb=" N   THR A  15 " --> pdb=" O   VAL A 205 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA A 206 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 445
      removed outlier: 6.848A  pdb=" N   LEU A 329 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 359 through 360
    Processing sheet with id=AA5, first strand: chain 'A' and resid 495 through 499
      removed outlier: 6.394A  pdb=" N   VAL A 496 " --> pdb=" O   ILE A 526 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   ASN A 528 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   THR A 498 " --> pdb=" O   ASN A 528 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   SER A 530 " --> pdb=" O   THR A 498 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   TRP A 525 " --> pdb=" O   ALA A 564 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   VAL A 566 " --> pdb=" O   TRP A 525 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   ILE A 527 " --> pdb=" O   VAL A 566 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    218 hydrogen bonds defined for protein.
    627 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.45

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1031
        1.33 -     1.45: 716
        1.45 -     1.57: 2520
        1.57 -     1.69: 6
        1.69 -     1.81: 20
  Bond restraints: 4293
  Sorted by residual:
  bond pdb=" N   VAL A 358 "
       pdb=" CA  VAL A 358 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.11e-02 8.12e+03 9.50e+00
  bond pdb=" N   PHE A   4 "
       pdb=" CA  PHE A   4 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.22e-02 6.72e+03 8.05e+00
  bond pdb=" N   LEU A   5 "
       pdb=" CA  LEU A   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.032 1.22e-02 6.72e+03 6.79e+00
  bond pdb=" N   GLY A 328 "
       pdb=" CA  GLY A 328 "
    ideal  model  delta    sigma   weight residual
    1.447  1.475 -0.028 1.08e-02 8.57e+03 6.77e+00
  bond pdb=" N   LEU A 174 "
       pdb=" CA  LEU A 174 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.32e-02 5.74e+03 6.32e+00
  ... (remaining 4288 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 5574
        1.21 -     2.42: 177
        2.42 -     3.63: 65
        3.63 -     4.83: 30
        4.83 -     6.04: 12
  Bond angle restraints: 5858
  Sorted by residual:
  angle pdb=" CA  VAL A 358 "
        pdb=" C   VAL A 358 "
        pdb=" O   VAL A 358 "
      ideal   model   delta    sigma   weight residual
     121.63  117.31    4.32 9.90e-01 1.02e+00 1.91e+01
  angle pdb=" CA  GLY A 326 "
        pdb=" C   GLY A 326 "
        pdb=" O   GLY A 326 "
      ideal   model   delta    sigma   weight residual
     122.47  118.12    4.35 1.08e+00 8.57e-01 1.62e+01
  angle pdb=" C   LEU A   7 "
        pdb=" N   PRO A   8 "
        pdb=" CA  PRO A   8 "
      ideal   model   delta    sigma   weight residual
     119.66  122.35   -2.69 7.20e-01 1.93e+00 1.39e+01
  angle pdb=" CA  GLY A 328 "
        pdb=" C   GLY A 328 "
        pdb=" O   GLY A 328 "
      ideal   model   delta    sigma   weight residual
     121.63  117.66    3.97 1.07e+00 8.73e-01 1.38e+01
  angle pdb=" C   ASN A 130 "
        pdb=" CA  ASN A 130 "
        pdb=" CB  ASN A 130 "
      ideal   model   delta    sigma   weight residual
     109.80  115.75   -5.95 1.65e+00 3.67e-01 1.30e+01
  ... (remaining 5853 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.35: 2365
       16.35 -    32.69: 173
       32.69 -    49.03: 44
       49.03 -    65.38: 19
       65.38 -    81.72: 5
  Dihedral angle restraints: 2606
    sinusoidal: 1023
      harmonic: 1583
  Sorted by residual:
  dihedral pdb=" C5' ADP A 601 "
           pdb=" O5' ADP A 601 "
           pdb=" PA  ADP A 601 "
           pdb=" O2A ADP A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   10.63  -70.63     1      2.00e+01 2.50e-03 1.60e+01
  dihedral pdb=" CG  ARG A 516 "
           pdb=" CD  ARG A 516 "
           pdb=" NE  ARG A 516 "
           pdb=" CZ  ARG A 516 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.25   44.75     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CB  MET A   2 "
           pdb=" CG  MET A   2 "
           pdb=" SD  MET A   2 "
           pdb=" CE  MET A   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  125.97   54.03     3      1.50e+01 4.44e-03 9.25e+00
  ... (remaining 2603 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 557
       0.041 -    0.083: 84
       0.083 -    0.124: 51
       0.124 -    0.165: 11
       0.165 -    0.206: 4
  Chirality restraints: 707
  Sorted by residual:
  chirality pdb=" CA  LEU A 360 "
            pdb=" N   LEU A 360 "
            pdb=" C   LEU A 360 "
            pdb=" CB  LEU A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  ASN A 246 "
            pdb=" N   ASN A 246 "
            pdb=" C   ASN A 246 "
            pdb=" CB  ASN A 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.26e-01
  chirality pdb=" CA  VAL A 358 "
            pdb=" N   VAL A 358 "
            pdb=" C   VAL A 358 "
            pdb=" CB  VAL A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.31e-01
  ... (remaining 704 not shown)

  Planarity restraints: 754
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 264 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO A 265 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 265 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 265 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  92 "    0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO A  93 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A  93 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  93 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 538 "   -0.019 5.00e-02 4.00e+02   2.93e-02 1.38e+00
        pdb=" N   PRO A 539 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 539 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 539 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 751 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 9
        2.53 -     3.13: 3385
        3.13 -     3.72: 6526
        3.72 -     4.31: 8305
        4.31 -     4.90: 14442
  Nonbonded interactions: 32667
  Sorted by model distance:
  nonbonded pdb=" O1B ADP A 602 "
            pdb="MG    MG A 604 "
     model   vdw
     1.943 2.170
  nonbonded pdb=" O3B ADP A 601 "
            pdb="MG    MG A 603 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" OD1 ASN A 130 "
            pdb=" N   ALA A 131 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" OG1 THR A  23 "
            pdb="MG    MG A 604 "
     model   vdw
     2.468 2.170
  nonbonded pdb=" O   ASP A 371 "
            pdb=" OG1 THR A 372 "
     model   vdw
     2.476 3.040
  ... (remaining 32662 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.890
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.830
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4293  Z= 0.212
  Angle     :  0.662   6.043   5858  Z= 0.377
  Chirality :  0.044   0.206    707
  Planarity :  0.004   0.045    754
  Dihedral  : 13.915  81.720   1576
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.39), residues: 544
  helix:  3.10 (0.31), residues: 263
  sheet: -2.65 (0.63), residues: 70
  loop : -0.25 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 152 
 TYR   0.006   0.001   TYR A 187 
 PHE   0.010   0.001   PHE A 121 
 TRP   0.004   0.001   TRP A 523 
 HIS   0.005   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4293)
  covalent geometry    : angle       0.66200 ( 5858)
  hydrogen bonds       : bond        0.16476 (  218)
  hydrogen bonds       : angle       5.77866 (  627)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A   31 ILE cc_start: 0.8903 (mm) cc_final: 0.8635 (mt)
REVERT: A   91 VAL cc_start: 0.8543 (t) cc_final: 0.7840 (t)
REVERT: A  156 LEU cc_start: 0.8172 (tp) cc_final: 0.7843 (tp)
REVERT: A  188 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7447 (tppp)
REVERT: A  258 GLN cc_start: 0.8419 (mm110) cc_final: 0.7486 (tt0)
REVERT: A  386 ASP cc_start: 0.8114 (t70) cc_final: 0.7522 (p0)
REVERT: A  390 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7705 (tp30)
REVERT: A  417 ASP cc_start: 0.8439 (t70) cc_final: 0.8033 (t0)
REVERT: A  434 ARG cc_start: 0.7315 (ptp-110) cc_final: 0.6446 (mtt90)
REVERT: A  446 MET cc_start: 0.8570 (mmt) cc_final: 0.7958 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0992
  time to fit residues: 15.1490
Evaluate side-chains
  71 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 186 GLN
A 210 GLN
A 263 ASN
A 559 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.164561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.132426 restraints weight = 5589.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.136772 restraints weight = 3678.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.139652 restraints weight = 2756.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.141946 restraints weight = 2247.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.143469 restraints weight = 1926.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4293  Z= 0.141
  Angle     :  0.664   9.495   5858  Z= 0.298
  Chirality :  0.042   0.181    707
  Planarity :  0.005   0.045    754
  Dihedral  :  5.691  70.545    606
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 12.30 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.38), residues: 544
  helix:  3.07 (0.30), residues: 267
  sheet: -2.59 (0.58), residues: 85
  loop : -0.06 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 290 
 TYR   0.004   0.001   TYR A  86 
 PHE   0.018   0.002   PHE A 121 
 TRP   0.004   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 4293)
  covalent geometry    : angle       0.66381 ( 5858)
  hydrogen bonds       : bond        0.03676 (  218)
  hydrogen bonds       : angle       4.21052 (  627)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   31 ILE cc_start: 0.9038 (mm) cc_final: 0.8617 (mt)
REVERT: A  188 LYS cc_start: 0.7962 (ttpt) cc_final: 0.7546 (tppp)
REVERT: A  258 GLN cc_start: 0.8472 (mm110) cc_final: 0.7453 (tt0)
REVERT: A  279 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7652 (mmtt)
REVERT: A  390 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7941 (tp30)
REVERT: A  417 ASP cc_start: 0.8316 (t70) cc_final: 0.8014 (t0)
REVERT: A  434 ARG cc_start: 0.7013 (ptp-110) cc_final: 0.6349 (mtt180)
REVERT: A  446 MET cc_start: 0.8524 (mmt) cc_final: 0.8096 (mmt)
  outliers start: 12
  outliers final: 6
  residues processed: 83
  average time/residue: 0.0761
  time to fit residues: 7.7813
Evaluate side-chains
  68 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  520 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 34 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 149 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.165247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.132844 restraints weight = 5486.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.137267 restraints weight = 3606.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.140305 restraints weight = 2694.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.142320 restraints weight = 2193.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.144074 restraints weight = 1894.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4293  Z= 0.118
  Angle     :  0.614   7.596   5858  Z= 0.271
  Chirality :  0.041   0.141    707
  Planarity :  0.004   0.043    754
  Dihedral  :  5.568  67.320    606
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.81 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.38), residues: 544
  helix:  3.14 (0.30), residues: 266
  sheet: -2.40 (0.57), residues: 85
  loop : -0.32 (0.46), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 384 
 TYR   0.011   0.001   TYR A 187 
 PHE   0.013   0.001   PHE A 121 
 TRP   0.003   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4293)
  covalent geometry    : angle       0.61369 ( 5858)
  hydrogen bonds       : bond        0.03056 (  218)
  hydrogen bonds       : angle       3.90249 (  627)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   31 ILE cc_start: 0.9003 (mm) cc_final: 0.8596 (mt)
REVERT: A   45 THR cc_start: 0.7436 (p) cc_final: 0.7105 (m)
REVERT: A  188 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7316 (mmtm)
REVERT: A  258 GLN cc_start: 0.8456 (mm110) cc_final: 0.7456 (tt0)
REVERT: A  279 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7698 (mmtt)
REVERT: A  390 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7951 (tp30)
REVERT: A  417 ASP cc_start: 0.8309 (t70) cc_final: 0.7953 (t0)
REVERT: A  434 ARG cc_start: 0.6918 (ptp-110) cc_final: 0.6259 (mtt180)
REVERT: A  446 MET cc_start: 0.8513 (mmt) cc_final: 0.8109 (mmt)
REVERT: A  484 MET cc_start: 0.7645 (ttp) cc_final: 0.7440 (ptm)
  outliers start: 11
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0502
  time to fit residues: 5.1376
Evaluate side-chains
  68 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  520 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 584 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.149542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.117524 restraints weight = 5648.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.121230 restraints weight = 3924.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.123794 restraints weight = 3045.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.125667 restraints weight = 2550.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.127039 restraints weight = 2244.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   4293  Z= 0.283
  Angle     :  0.754   7.773   5858  Z= 0.348
  Chirality :  0.046   0.155    707
  Planarity :  0.005   0.047    754
  Dihedral  :  6.310  78.573    606
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 16.40 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.36), residues: 544
  helix:  2.48 (0.29), residues: 266
  sheet: -2.54 (0.61), residues: 64
  loop : -0.89 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 184 
 TYR   0.009   0.002   TYR A 187 
 PHE   0.015   0.002   PHE A 432 
 TRP   0.007   0.002   TRP A 160 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00670 ( 4293)
  covalent geometry    : angle       0.75351 ( 5858)
  hydrogen bonds       : bond        0.04253 (  218)
  hydrogen bonds       : angle       4.23918 (  627)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A   45 THR cc_start: 0.7784 (p) cc_final: 0.7564 (m)
REVERT: A  108 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7333 (mt-10)
REVERT: A  188 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7393 (mmtm)
REVERT: A  258 GLN cc_start: 0.8552 (mm110) cc_final: 0.7438 (tt0)
REVERT: A  390 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8093 (tp30)
REVERT: A  417 ASP cc_start: 0.8447 (t70) cc_final: 0.8082 (t0)
REVERT: A  434 ARG cc_start: 0.7068 (ptp-110) cc_final: 0.6276 (mtt180)
REVERT: A  435 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8016 (tt)
REVERT: A  446 MET cc_start: 0.8604 (mmt) cc_final: 0.8249 (mmt)
  outliers start: 19
  outliers final: 14
  residues processed: 75
  average time/residue: 0.0450
  time to fit residues: 4.4705
Evaluate side-chains
  71 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  529 THR
Chi-restraints excluded: chain A residue  568 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 42 optimal weight:    0.4980
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.157345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.124855 restraints weight = 5567.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.128849 restraints weight = 3765.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.131680 restraints weight = 2867.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.133721 restraints weight = 2356.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.135261 restraints weight = 2046.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4293  Z= 0.121
  Angle     :  0.625   7.580   5858  Z= 0.276
  Chirality :  0.040   0.138    707
  Planarity :  0.004   0.044    754
  Dihedral  :  5.921  71.259    606
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.08 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.37), residues: 544
  helix:  2.87 (0.29), residues: 266
  sheet: -2.75 (0.56), residues: 73
  loop : -0.62 (0.42), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 290 
 TYR   0.004   0.001   TYR A 187 
 PHE   0.018   0.001   PHE A 429 
 TRP   0.005   0.001   TRP A 525 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4293)
  covalent geometry    : angle       0.62476 ( 5858)
  hydrogen bonds       : bond        0.02971 (  218)
  hydrogen bonds       : angle       3.83679 (  627)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A   31 ILE cc_start: 0.9007 (mm) cc_final: 0.8603 (mt)
REVERT: A  108 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7254 (mt-10)
REVERT: A  156 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8219 (mp)
REVERT: A  188 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7337 (mmtm)
REVERT: A  258 GLN cc_start: 0.8457 (mm110) cc_final: 0.7400 (tt0)
REVERT: A  390 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7994 (tp30)
REVERT: A  417 ASP cc_start: 0.8432 (t70) cc_final: 0.8084 (t0)
REVERT: A  434 ARG cc_start: 0.7080 (ptp-110) cc_final: 0.6267 (mtt180)
REVERT: A  435 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7937 (tt)
REVERT: A  446 MET cc_start: 0.8449 (mmt) cc_final: 0.8109 (mmt)
REVERT: A  484 MET cc_start: 0.7808 (ttp) cc_final: 0.7596 (ptm)
  outliers start: 13
  outliers final: 8
  residues processed: 78
  average time/residue: 0.0581
  time to fit residues: 5.8818
Evaluate side-chains
  75 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  520 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0970
   chunk 36 optimal weight:    0.7980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.155558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.123788 restraints weight = 5625.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.127673 restraints weight = 3819.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.130388 restraints weight = 2909.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.132166 restraints weight = 2395.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.133793 restraints weight = 2091.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4293  Z= 0.158
  Angle     :  0.653   7.991   5858  Z= 0.288
  Chirality :  0.041   0.144    707
  Planarity :  0.004   0.044    754
  Dihedral  :  5.934  72.775    606
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.00 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.36), residues: 544
  helix:  2.81 (0.30), residues: 266
  sheet: -2.81 (0.56), residues: 70
  loop : -0.63 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  62 
 TYR   0.004   0.001   TYR A 187 
 PHE   0.016   0.001   PHE A 429 
 TRP   0.004   0.001   TRP A 523 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 4293)
  covalent geometry    : angle       0.65268 ( 5858)
  hydrogen bonds       : bond        0.03182 (  218)
  hydrogen bonds       : angle       3.81510 (  627)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A   31 ILE cc_start: 0.9034 (mm) cc_final: 0.8615 (mt)
REVERT: A  108 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7234 (mt-10)
REVERT: A  156 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8254 (mp)
REVERT: A  177 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8680 (tp)
REVERT: A  188 LYS cc_start: 0.7957 (ttpt) cc_final: 0.7298 (mmtm)
REVERT: A  258 GLN cc_start: 0.8485 (mm110) cc_final: 0.7388 (tt0)
REVERT: A  390 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8022 (tp30)
REVERT: A  417 ASP cc_start: 0.8410 (t70) cc_final: 0.8046 (t0)
REVERT: A  434 ARG cc_start: 0.7162 (ptp-110) cc_final: 0.6316 (mtt180)
REVERT: A  435 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8039 (tt)
REVERT: A  446 MET cc_start: 0.8458 (mmt) cc_final: 0.8134 (mmt)
  outliers start: 14
  outliers final: 10
  residues processed: 75
  average time/residue: 0.0644
  time to fit residues: 6.1551
Evaluate side-chains
  77 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  529 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.154832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.122330 restraints weight = 5651.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.126188 restraints weight = 3846.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.128889 restraints weight = 2945.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.130901 restraints weight = 2434.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.132325 restraints weight = 2117.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4293  Z= 0.173
  Angle     :  0.661   7.155   5858  Z= 0.294
  Chirality :  0.042   0.173    707
  Planarity :  0.004   0.045    754
  Dihedral  :  6.041  73.580    606
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 17.54 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.36), residues: 544
  helix:  2.73 (0.30), residues: 266
  sheet: -2.80 (0.56), residues: 70
  loop : -0.66 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  62 
 TYR   0.005   0.001   TYR A 187 
 PHE   0.016   0.001   PHE A 429 
 TRP   0.005   0.001   TRP A 523 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 4293)
  covalent geometry    : angle       0.66115 ( 5858)
  hydrogen bonds       : bond        0.03277 (  218)
  hydrogen bonds       : angle       3.85720 (  627)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   31 ILE cc_start: 0.9044 (mm) cc_final: 0.8633 (mt)
REVERT: A  108 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7243 (mt-10)
REVERT: A  156 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8269 (mp)
REVERT: A  177 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8681 (tp)
REVERT: A  188 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7285 (mmtm)
REVERT: A  258 GLN cc_start: 0.8500 (mm110) cc_final: 0.7351 (tt0)
REVERT: A  390 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8034 (tp30)
REVERT: A  416 GLU cc_start: 0.8564 (tp30) cc_final: 0.8358 (tp30)
REVERT: A  417 ASP cc_start: 0.8446 (t70) cc_final: 0.8126 (t0)
REVERT: A  434 ARG cc_start: 0.7222 (ptp-110) cc_final: 0.6384 (mtt180)
REVERT: A  435 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8080 (tt)
REVERT: A  446 MET cc_start: 0.8461 (mmt) cc_final: 0.8103 (mmt)
  outliers start: 17
  outliers final: 13
  residues processed: 78
  average time/residue: 0.0426
  time to fit residues: 4.3352
Evaluate side-chains
  81 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  529 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0170
   chunk 36 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0970
   chunk 50 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.5016

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.159025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.127091 restraints weight = 5541.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.131098 restraints weight = 3729.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.133981 restraints weight = 2822.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.136070 restraints weight = 2310.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.137488 restraints weight = 1994.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4293  Z= 0.106
  Angle     :  0.616   8.553   5858  Z= 0.268
  Chirality :  0.040   0.150    707
  Planarity :  0.004   0.043    754
  Dihedral  :  5.726  66.878    606
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.45 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.37), residues: 544
  helix:  2.82 (0.30), residues: 268
  sheet: -2.72 (0.55), residues: 74
  loop : -0.52 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  62 
 TYR   0.003   0.000   TYR A 187 
 PHE   0.013   0.001   PHE A 429 
 TRP   0.005   0.001   TRP A 525 
 HIS   0.003   0.000   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 4293)
  covalent geometry    : angle       0.61637 ( 5858)
  hydrogen bonds       : bond        0.02747 (  218)
  hydrogen bonds       : angle       3.70987 (  627)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A    2 MET cc_start: 0.7751 (mmm) cc_final: 0.7357 (mtt)
REVERT: A   31 ILE cc_start: 0.8989 (mm) cc_final: 0.8584 (mt)
REVERT: A  108 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7205 (mt-10)
REVERT: A  188 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7220 (mmtm)
REVERT: A  258 GLN cc_start: 0.8448 (mm110) cc_final: 0.7278 (tt0)
REVERT: A  390 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7948 (tp30)
REVERT: A  417 ASP cc_start: 0.8411 (t70) cc_final: 0.8117 (t0)
REVERT: A  446 MET cc_start: 0.8398 (mmt) cc_final: 0.7966 (mmt)
  outliers start: 13
  outliers final: 11
  residues processed: 81
  average time/residue: 0.0406
  time to fit residues: 4.3259
Evaluate side-chains
  78 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  529 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 52 optimal weight:    0.2980
   chunk 17 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.158167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.126214 restraints weight = 5623.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.130209 restraints weight = 3794.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.133095 restraints weight = 2875.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.134932 restraints weight = 2363.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136415 restraints weight = 2057.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4293  Z= 0.119
  Angle     :  0.630   8.410   5858  Z= 0.276
  Chirality :  0.040   0.149    707
  Planarity :  0.004   0.043    754
  Dihedral  :  5.716  67.548    606
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.13 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.37), residues: 544
  helix:  2.86 (0.30), residues: 266
  sheet: -2.52 (0.55), residues: 72
  loop : -0.60 (0.42), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  62 
 TYR   0.003   0.001   TYR A 187 
 PHE   0.012   0.001   PHE A 429 
 TRP   0.004   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4293)
  covalent geometry    : angle       0.63031 ( 5858)
  hydrogen bonds       : bond        0.02850 (  218)
  hydrogen bonds       : angle       3.68717 (  627)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   31 ILE cc_start: 0.8998 (mm) cc_final: 0.8591 (mt)
REVERT: A  108 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7166 (mt-10)
REVERT: A  188 LYS cc_start: 0.7894 (ttpt) cc_final: 0.7209 (mmtm)
REVERT: A  258 GLN cc_start: 0.8458 (mm110) cc_final: 0.7279 (tt0)
REVERT: A  333 MET cc_start: 0.8063 (ttm) cc_final: 0.7843 (ttp)
REVERT: A  390 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7971 (tp30)
REVERT: A  416 GLU cc_start: 0.8542 (tp30) cc_final: 0.8321 (tp30)
REVERT: A  417 ASP cc_start: 0.8371 (t70) cc_final: 0.8116 (t0)
REVERT: A  446 MET cc_start: 0.8433 (mmt) cc_final: 0.8073 (mmt)
  outliers start: 12
  outliers final: 11
  residues processed: 74
  average time/residue: 0.0573
  time to fit residues: 5.4787
Evaluate side-chains
  75 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  529 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0170
   chunk 42 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0870
   chunk 3 optimal weight:    0.7980
   chunk 23 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.151069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.124268 restraints weight = 5422.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.126964 restraints weight = 4076.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.128974 restraints weight = 3312.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.130320 restraints weight = 2840.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.131435 restraints weight = 2535.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4293  Z= 0.109
  Angle     :  0.632   8.477   5858  Z= 0.275
  Chirality :  0.040   0.157    707
  Planarity :  0.004   0.042    754
  Dihedral  :  5.660  64.480    606
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.50 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.37), residues: 544
  helix:  2.92 (0.30), residues: 266
  sheet: -2.51 (0.55), residues: 74
  loop : -0.50 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  62 
 TYR   0.003   0.001   TYR A 187 
 PHE   0.012   0.001   PHE A 429 
 TRP   0.004   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4293)
  covalent geometry    : angle       0.63166 ( 5858)
  hydrogen bonds       : bond        0.02719 (  218)
  hydrogen bonds       : angle       3.64030 (  627)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 ILE cc_start: 0.8970 (mm) cc_final: 0.8573 (mt)
REVERT: A  108 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7200 (mt-10)
REVERT: A  188 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7188 (mmtm)
REVERT: A  258 GLN cc_start: 0.8440 (mm110) cc_final: 0.7248 (tt0)
REVERT: A  333 MET cc_start: 0.8084 (ttm) cc_final: 0.7832 (ttp)
REVERT: A  390 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7941 (tp30)
REVERT: A  417 ASP cc_start: 0.8390 (t70) cc_final: 0.8142 (t0)
REVERT: A  446 MET cc_start: 0.8425 (mmt) cc_final: 0.8017 (mmt)
  outliers start: 10
  outliers final: 10
  residues processed: 72
  average time/residue: 0.0450
  time to fit residues: 4.1937
Evaluate side-chains
  73 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  520 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0980
   chunk 37 optimal weight:    0.8980
   chunk 5 optimal weight:    0.1980
   chunk 13 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.151518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.124721 restraints weight = 5466.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.127465 restraints weight = 4094.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.129417 restraints weight = 3315.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.130946 restraints weight = 2834.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.131680 restraints weight = 2519.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.4016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4293  Z= 0.112
  Angle     :  0.642   8.742   5858  Z= 0.280
  Chirality :  0.040   0.158    707
  Planarity :  0.004   0.042    754
  Dihedral  :  5.476  63.757    606
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 20.27 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.37), residues: 544
  helix:  2.89 (0.30), residues: 266
  sheet: -2.45 (0.56), residues: 74
  loop : -0.43 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  62 
 TYR   0.003   0.001   TYR A 187 
 PHE   0.011   0.001   PHE A 121 
 TRP   0.003   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 4293)
  covalent geometry    : angle       0.64188 ( 5858)
  hydrogen bonds       : bond        0.02690 (  218)
  hydrogen bonds       : angle       3.62160 (  627)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 764.52 seconds
wall clock time: 13 minutes 50.49 seconds (830.49 seconds total)