Starting phenix.real_space_refine
on Tue Aug  4 14:23:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yql_73339/08_2026/9yql_73339.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yql_73339/08_2026/9yql_73339.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yql_73339/08_2026/9yql_73339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yql_73339/08_2026/9yql_73339.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yql_73339/08_2026/9yql_73339.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yql_73339/08_2026/9yql_73339.cif"
  }
  resolution = 3.57
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    2392      2.51       5
     N     644      2.21       5
     O     732      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3794
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 3794
          Classifications: {'peptide': 476}
          Link IDs: {'PTRANS': 13, 'TRANS': 462}
          Chain breaks: 1
  Time building chain proxies: 0.68, per 1000 atoms: 0.18
  Number of scatterers: 3794
  At special positions: 0
  Unit cell: (65.728, 69.888, 114.816, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      26     16.00
     O     732      8.00
     N     644      7.00
     C    2392      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: 0.24
  Conformation dependent library (CDL) restraints added in 130.3 milliseconds
  

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  916

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      85.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 109 through 128
    Processing helix  chain 'A' and resid 130 through 144
      removed outlier: 3.706A  pdb=" N   ILE A 134 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   GLU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ALA A 140 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 165
      removed outlier: 3.705A  pdb=" N   LEU A 152 " --> pdb=" O   LYS A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 183
    Processing helix  chain 'A' and resid 186 through 200
      removed outlier: 3.643A  pdb=" N   LEU A 190 " --> pdb=" O   TYR A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 218
      removed outlier: 3.985A  pdb=" N   CYS A 206 " --> pdb=" O   ASN A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 245
      removed outlier: 4.047A  pdb=" N   MET A 225 " --> pdb=" O   ASN A 221 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS A 245 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 262
    Processing helix  chain 'A' and resid 298 through 307
    Processing helix  chain 'A' and resid 312 through 323
      removed outlier: 3.512A  pdb=" N   ALA A 323 " --> pdb=" O   LYS A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 342
    Processing helix  chain 'A' and resid 344 through 358
      Proline residue:  A 350  - end of helix
    Processing helix  chain 'A' and resid 362 through 380
    Processing helix  chain 'A' and resid 382 through 397
      removed outlier: 3.903A  pdb=" N   SER A 386 " --> pdb=" O   GLN A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 415
      removed outlier: 3.670A  pdb=" N   TYR A 404 " --> pdb=" O   ASN A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 431
    Processing helix  chain 'A' and resid 434 through 452
      removed outlier: 3.645A  pdb=" N   GLY A 452 " --> pdb=" O   GLN A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 472
      removed outlier: 4.004A  pdb=" N   ILE A 458 " --> pdb=" O   ASN A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 488
      removed outlier: 3.894A  pdb=" N   TYR A 479 " --> pdb=" O   CYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 506
      removed outlier: 4.170A  pdb=" N   GLU A 497 " --> pdb=" O   GLY A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 522
    Processing helix  chain 'A' and resid 526 through 541
    Processing helix  chain 'A' and resid 544 through 559
    Processing helix  chain 'A' and resid 560 through 574
      removed outlier: 3.732A  pdb=" N   ALA A 564 " --> pdb=" O   ASN A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 602

    289 hydrogen bonds defined for protein.
    867 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: 0.35

  Time building geometry restraints manager: 0.32 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: 838
        1.33 -     1.45: 786
        1.45 -     1.58: 2191
        1.58 -     1.70: 0
        1.70 -     1.82: 40
  Bond restraints: 3855
  Sorted by residual:
  bond pdb=" CA  PHE A 546 "
       pdb=" C   PHE A 546 "
    ideal  model  delta    sigma   weight residual
    1.524  1.478  0.046 1.26e-02 6.30e+03 1.32e+01
  bond pdb=" CA  LEU A 413 "
       pdb=" C   LEU A 413 "
    ideal  model  delta    sigma   weight residual
    1.524  1.484  0.039 1.29e-02 6.01e+03 9.17e+00
  bond pdb=" C   PHE A 546 "
       pdb=" O   PHE A 546 "
    ideal  model  delta    sigma   weight residual
    1.237  1.208  0.029 1.16e-02 7.43e+03 6.14e+00
  bond pdb=" C   PHE A 546 "
       pdb=" N   ALA A 547 "
    ideal  model  delta    sigma   weight residual
    1.334  1.305  0.029 1.27e-02 6.20e+03 5.20e+00
  bond pdb=" C   LEU A 413 "
       pdb=" O   LEU A 413 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.026 1.19e-02 7.06e+03 4.86e+00
  ... (remaining 3850 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 5081
        2.13 -     4.26: 75
        4.26 -     6.39: 18
        6.39 -     8.52: 3
        8.52 -    10.65: 3
  Bond angle restraints: 5180
  Sorted by residual:
  angle pdb=" CB  LYS A 185 "
        pdb=" CG  LYS A 185 "
        pdb=" CD  LYS A 185 "
      ideal   model   delta    sigma   weight residual
     111.30  120.13   -8.83 2.30e+00 1.89e-01 1.47e+01
  angle pdb=" N   ILE A 268 "
        pdb=" CA  ILE A 268 "
        pdb=" C   ILE A 268 "
      ideal   model   delta    sigma   weight residual
     111.00  115.13   -4.13 1.09e+00 8.42e-01 1.43e+01
  angle pdb=" CA  LYS A 185 "
        pdb=" CB  LYS A 185 "
        pdb=" CG  LYS A 185 "
      ideal   model   delta    sigma   weight residual
     114.10  121.66   -7.56 2.00e+00 2.50e-01 1.43e+01
  angle pdb=" CA  GLN A 167 "
        pdb=" CB  GLN A 167 "
        pdb=" CG  GLN A 167 "
      ideal   model   delta    sigma   weight residual
     114.10  121.45   -7.35 2.00e+00 2.50e-01 1.35e+01
  angle pdb=" N   PHE A 546 "
        pdb=" CA  PHE A 546 "
        pdb=" C   PHE A 546 "
      ideal   model   delta    sigma   weight residual
     111.14  107.24    3.90 1.08e+00 8.57e-01 1.30e+01
  ... (remaining 5175 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 2051
       17.37 -    34.73: 237
       34.73 -    52.10: 90
       52.10 -    69.46: 14
       69.46 -    86.83: 7
  Dihedral angle restraints: 2399
    sinusoidal: 986
      harmonic: 1413
  Sorted by residual:
  dihedral pdb=" CA  LYS A 168 "
           pdb=" C   LYS A 168 "
           pdb=" N   TRP A 169 "
           pdb=" CA  TRP A 169 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.58  -26.42     0      5.00e+00 4.00e-02 2.79e+01
  dihedral pdb=" CA  LYS A 129 "
           pdb=" C   LYS A 129 "
           pdb=" N   TYR A 130 "
           pdb=" CA  TYR A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.06  -20.94     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CB  GLU A 419 "
           pdb=" CG  GLU A 419 "
           pdb=" CD  GLU A 419 "
           pdb=" OE1 GLU A 419 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.83   86.83     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 2396 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 441
       0.045 -    0.090: 91
       0.090 -    0.136: 24
       0.136 -    0.181: 1
       0.181 -    0.226: 2
  Chirality restraints: 559
  Sorted by residual:
  chirality pdb=" CA  GLN A 380 "
            pdb=" N   GLN A 380 "
            pdb=" C   GLN A 380 "
            pdb=" CB  GLN A 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  GLN A 167 "
            pdb=" N   GLN A 167 "
            pdb=" C   GLN A 167 "
            pdb=" CB  GLN A 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.20e-01
  chirality pdb=" CG  LEU A 232 "
            pdb=" CB  LEU A 232 "
            pdb=" CD1 LEU A 232 "
            pdb=" CD2 LEU A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.68e-01
  ... (remaining 556 not shown)

  Planarity restraints: 678
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 382 "    0.052 5.00e-02 4.00e+02   7.92e-02 1.00e+01
        pdb=" N   PRO A 383 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO A 383 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 383 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 545 "    0.010 2.00e-02 2.50e+03   1.94e-02 3.78e+00
        pdb=" C   ASP A 545 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ASP A 545 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE A 546 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 382 "    0.009 2.00e-02 2.50e+03   1.68e-02 2.83e+00
        pdb=" C   GLN A 382 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   GLN A 382 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PRO A 383 "    0.010 2.00e-02 2.50e+03
  ... (remaining 675 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 1376
        2.87 -     3.38: 3980
        3.38 -     3.89: 6262
        3.89 -     4.39: 6656
        4.39 -     4.90: 11121
  Nonbonded interactions: 29395
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 312 "
            pdb=" OG  SER A 315 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   ASN A 542 "
            pdb=" OH  TYR A 548 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" O   PRO A 383 "
            pdb=" OG  SER A 386 "
     model   vdw
     2.413 3.040
  nonbonded pdb=" OD1 ASN A 109 "
            pdb=" N   ASP A 112 "
     model   vdw
     2.427 3.120
  nonbonded pdb=" NZ  LYS A 118 "
            pdb=" OD1 ASN A 119 "
     model   vdw
     2.438 3.120
  ... (remaining 29390 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:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     3.840
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
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      :  0.004   0.053   3855  Z= 0.201
  Angle     :  0.706  10.648   5180  Z= 0.374
  Chirality :  0.041   0.226    559
  Planarity :  0.005   0.079    678
  Dihedral  : 17.617  86.830   1483
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 2.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 27.36 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.50 (0.39), residues: 472
  helix:  1.49 (0.26), residues: 396
  sheet:  None (None), residues: 0
  loop : -1.56 (0.61), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 474 
 TYR   0.012   0.001   TYR A 482 
 PHE   0.009   0.001   PHE A 338 
 TRP   0.004   0.001   TRP A 169 
 HIS   0.002   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.20 ( 3855)
  covalent geometry    : angle       0.70633 /  0.37 ( 5180)
  hydrogen bonds       : bond        0.11763 /  7.40 (  289)
  hydrogen bonds       : angle       5.06349 /  3.68 (  867)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8344 (tttt) cc_final: 0.7951 (tttt)
REVERT: A  234 LEU cc_start: 0.7605 (mp) cc_final: 0.7306 (mp)
REVERT: A  364 LYS cc_start: 0.7596 (mmtp) cc_final: 0.7133 (mmtp)
REVERT: A  462 MET cc_start: 0.6951 (mmm) cc_final: 0.6575 (mmm)
REVERT: A  539 GLU cc_start: 0.7373 (tt0) cc_final: 0.7071 (tp30)
REVERT: A  549 GLU cc_start: 0.5953 (tm-30) cc_final: 0.5488 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 117
  average time/residue: 0.0635
  time to fit residues: 8.8562
Evaluate side-chains
  117 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0970
   overall best weight:    0.5178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 165 GLN
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.140977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.125701 restraints weight = 7311.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.129586 restraints weight = 3865.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.132177 restraints weight = 2341.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.133933 restraints weight = 1550.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.135043 restraints weight = 1097.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3855  Z= 0.160
  Angle     :  0.535   8.120   5180  Z= 0.281
  Chirality :  0.037   0.176    559
  Planarity :  0.004   0.067    678
  Dihedral  :  4.797  54.306    516
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 26.12 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.27 (0.38), residues: 472
  helix:  2.02 (0.25), residues: 401
  sheet:  None (None), residues: 0
  loop : -1.53 (0.66), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 474 
 TYR   0.009   0.001   TYR A 304 
 PHE   0.010   0.001   PHE A 568 
 TRP   0.003   0.001   TRP A 169 
 HIS   0.002   0.000   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.16 ( 3855)
  covalent geometry    : angle       0.53526 /  0.28 ( 5180)
  hydrogen bonds       : bond        0.03823 /  2.48 (  289)
  hydrogen bonds       : angle       3.93936 /  2.90 (  867)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: A  220 GLN cc_start: 0.8585 (mp10) cc_final: 0.8365 (mp10)
REVERT: A  462 MET cc_start: 0.7001 (mmm) cc_final: 0.6793 (mmm)
REVERT: A  549 GLU cc_start: 0.6270 (tm-30) cc_final: 0.5569 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 121
  average time/residue: 0.0612
  time to fit residues: 8.7958
Evaluate side-chains
  116 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LYS
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  533 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    0.2980
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0870
   chunk 41 optimal weight:    0.9990
   chunk 3 optimal weight:    0.3980
   chunk 40 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.3758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 122 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.141615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.126402 restraints weight = 7271.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.130218 restraints weight = 3854.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.132781 restraints weight = 2339.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.134467 restraints weight = 1555.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.135683 restraints weight = 1112.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3855  Z= 0.133
  Angle     :  0.527   7.991   5180  Z= 0.273
  Chirality :  0.036   0.144    559
  Planarity :  0.003   0.053    678
  Dihedral  :  4.809  58.021    516
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 28.86 %
    Favored  : 69.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.38), residues: 472
  helix:  2.10 (0.25), residues: 401
  sheet:  None (None), residues: 0
  loop : -1.41 (0.68), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 474 
 TYR   0.007   0.001   TYR A 327 
 PHE   0.010   0.001   PHE A 338 
 TRP   0.002   0.001   TRP A 523 
 HIS   0.003   0.001   HIS A 592 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 3855)
  covalent geometry    : angle       0.52679 /  0.27 ( 5180)
  hydrogen bonds       : bond        0.03545 /  2.32 (  289)
  hydrogen bonds       : angle       3.81842 /  2.81 (  867)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLN cc_start: 0.7696 (mp10) cc_final: 0.7458 (mp10)
REVERT: A  230 LYS cc_start: 0.8394 (tttt) cc_final: 0.7906 (ttpt)
REVERT: A  294 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7279 (tm-30)
REVERT: A  324 GLU cc_start: 0.6917 (mp0) cc_final: 0.6659 (pm20)
REVERT: A  359 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.8012 (ptmt)
REVERT: A  378 MET cc_start: 0.7706 (tpp) cc_final: 0.7437 (tpt)
REVERT: A  462 MET cc_start: 0.7035 (mmm) cc_final: 0.6830 (mmm)
REVERT: A  520 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7239 (tm-30)
REVERT: A  539 GLU cc_start: 0.7467 (tt0) cc_final: 0.7199 (tt0)
REVERT: A  549 GLU cc_start: 0.6231 (tm-30) cc_final: 0.5502 (tm-30)
REVERT: A  555 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6938 (mm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 115
  average time/residue: 0.0565
  time to fit residues: 7.8296
Evaluate side-chains
  119 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LYS
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  359 LYS
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  533 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.6380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.139679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.124581 restraints weight = 7305.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.128353 restraints weight = 3834.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.130852 restraints weight = 2322.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.132598 restraints weight = 1546.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.133802 restraints weight = 1096.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3855  Z= 0.183
  Angle     :  0.556   8.590   5180  Z= 0.293
  Chirality :  0.038   0.158    559
  Planarity :  0.004   0.046    678
  Dihedral  :  4.920  58.776    516
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 30.10 %
    Favored  : 66.17 %
  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:  2.18 (0.38), residues: 472
  helix:  1.91 (0.25), residues: 405
  sheet:  None (None), residues: 0
  loop : -1.45 (0.71), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 447 
 TYR   0.011   0.001   TYR A 482 
 PHE   0.008   0.001   PHE A 338 
 TRP   0.002   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 592 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00392 /  0.18 ( 3855)
  covalent geometry    : angle       0.55623 /  0.29 ( 5180)
  hydrogen bonds       : bond        0.03826 /  2.50 (  289)
  hydrogen bonds       : angle       4.01138 /  2.95 (  867)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLN cc_start: 0.7861 (mp10) cc_final: 0.7591 (mp10)
REVERT: A  229 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.6417 (t0)
REVERT: A  230 LYS cc_start: 0.8384 (tttt) cc_final: 0.7892 (ttpt)
REVERT: A  233 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7250 (mmtp)
REVERT: A  294 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7567 (tm-30)
REVERT: A  324 GLU cc_start: 0.7289 (mp0) cc_final: 0.7070 (mp0)
REVERT: A  359 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7995 (ptmt)
REVERT: A  378 MET cc_start: 0.7738 (tpp) cc_final: 0.7463 (tpt)
REVERT: A  462 MET cc_start: 0.7016 (mmm) cc_final: 0.6770 (mmm)
REVERT: A  520 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7252 (tm-30)
REVERT: A  549 GLU cc_start: 0.6312 (tm-30) cc_final: 0.5553 (tm-30)
REVERT: A  561 MET cc_start: 0.7356 (mmm) cc_final: 0.6926 (tpp)
REVERT: A  599 LYS cc_start: 0.8500 (tptm) cc_final: 0.8276 (tptp)
  outliers start: 15
  outliers final: 8
  residues processed: 123
  average time/residue: 0.0574
  time to fit residues: 8.6337
Evaluate side-chains
  120 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  359 LYS
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  538 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.139119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.123832 restraints weight = 7228.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.127616 restraints weight = 3794.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.130194 restraints weight = 2305.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.131879 restraints weight = 1535.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.133151 restraints weight = 1101.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3855  Z= 0.200
  Angle     :  0.566   8.733   5180  Z= 0.298
  Chirality :  0.039   0.169    559
  Planarity :  0.004   0.037    678
  Dihedral  :  4.275  27.654    512
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 30.85 %
    Favored  : 64.93 %
  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:  1.97 (0.38), residues: 472
  helix:  1.74 (0.25), residues: 406
  sheet:  None (None), residues: 0
  loop : -1.37 (0.72), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 192 
 TYR   0.011   0.001   TYR A 298 
 PHE   0.011   0.002   PHE A 568 
 TRP   0.003   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 592 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.20 ( 3855)
  covalent geometry    : angle       0.56565 /  0.30 ( 5180)
  hydrogen bonds       : bond        0.03909 /  2.55 (  289)
  hydrogen bonds       : angle       4.06117 /  2.99 (  867)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  167 GLN cc_start: 0.8033 (mp10) cc_final: 0.7829 (mp10)
REVERT: A  230 LYS cc_start: 0.8381 (tttt) cc_final: 0.7867 (ttpt)
REVERT: A  233 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7775 (mmtp)
REVERT: A  296 SER cc_start: 0.5929 (OUTLIER) cc_final: 0.5288 (m)
REVERT: A  349 LYS cc_start: 0.8276 (ttpt) cc_final: 0.8076 (ttpt)
REVERT: A  378 MET cc_start: 0.7705 (tpp) cc_final: 0.7490 (tpt)
REVERT: A  430 LEU cc_start: 0.6501 (tp) cc_final: 0.6026 (tp)
REVERT: A  462 MET cc_start: 0.7084 (mmm) cc_final: 0.6801 (mmm)
REVERT: A  520 GLN cc_start: 0.7856 (tp-100) cc_final: 0.7281 (tm-30)
REVERT: A  526 ASP cc_start: 0.6227 (m-30) cc_final: 0.5906 (m-30)
REVERT: A  549 GLU cc_start: 0.6368 (tm-30) cc_final: 0.5600 (tm-30)
REVERT: A  555 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6920 (mm-30)
REVERT: A  604 LYS cc_start: 0.8085 (mttt) cc_final: 0.7486 (mptt)
  outliers start: 17
  outliers final: 10
  residues processed: 124
  average time/residue: 0.0562
  time to fit residues: 8.5411
Evaluate side-chains
  123 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  538 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 24 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    0.2980
   chunk 7 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN
A 594 GLN

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 = 0.139685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.124738 restraints weight = 7343.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.128523 restraints weight = 3886.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.131054 restraints weight = 2361.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.132841 restraints weight = 1582.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.134109 restraints weight = 1125.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3855  Z= 0.161
  Angle     :  0.576   9.278   5180  Z= 0.295
  Chirality :  0.039   0.163    559
  Planarity :  0.003   0.033    678
  Dihedral  :  4.202  27.084    512
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 31.59 %
    Favored  : 64.18 %
  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:  2.11 (0.38), residues: 472
  helix:  1.84 (0.25), residues: 406
  sheet:  None (None), residues: 0
  loop : -1.36 (0.71), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 192 
 TYR   0.009   0.001   TYR A 298 
 PHE   0.009   0.001   PHE A 338 
 TRP   0.002   0.001   TRP A 169 
 HIS   0.003   0.001   HIS A 592 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.16 ( 3855)
  covalent geometry    : angle       0.57592 /  0.30 ( 5180)
  hydrogen bonds       : bond        0.03683 /  2.41 (  289)
  hydrogen bonds       : angle       3.96624 /  2.92 (  867)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8344 (tttt) cc_final: 0.7875 (ttpt)
REVERT: A  233 LYS cc_start: 0.8289 (mmtm) cc_final: 0.7616 (mmtm)
REVERT: A  296 SER cc_start: 0.5872 (OUTLIER) cc_final: 0.5090 (p)
REVERT: A  378 MET cc_start: 0.7707 (tpp) cc_final: 0.7487 (tpt)
REVERT: A  430 LEU cc_start: 0.6457 (tp) cc_final: 0.6009 (tp)
REVERT: A  462 MET cc_start: 0.7070 (mmm) cc_final: 0.6791 (mmm)
REVERT: A  549 GLU cc_start: 0.6358 (tm-30) cc_final: 0.5543 (tm-30)
REVERT: A  561 MET cc_start: 0.7387 (tpp) cc_final: 0.7173 (mmm)
REVERT: A  604 LYS cc_start: 0.8074 (mttt) cc_final: 0.7476 (mptt)
  outliers start: 17
  outliers final: 12
  residues processed: 126
  average time/residue: 0.0472
  time to fit residues: 7.3323
Evaluate side-chains
  127 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  538 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0470
   chunk 36 optimal weight:    0.4980
   chunk 41 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0070
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.3696

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 594 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.140860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.125919 restraints weight = 7447.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.129772 restraints weight = 3910.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.132397 restraints weight = 2360.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.134128 restraints weight = 1550.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.135429 restraints weight = 1097.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3855  Z= 0.134
  Angle     :  0.578   9.737   5180  Z= 0.290
  Chirality :  0.038   0.152    559
  Planarity :  0.003   0.032    678
  Dihedral  :  4.068  25.579    512
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 32.84 %
    Favored  : 63.68 %
  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:  2.37 (0.38), residues: 472
  helix:  2.03 (0.25), residues: 402
  sheet:  None (None), residues: 0
  loop : -1.18 (0.71), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 192 
 TYR   0.007   0.001   TYR A 482 
 PHE   0.008   0.001   PHE A 338 
 TRP   0.002   0.001   TRP A 169 
 HIS   0.003   0.001   HIS A 592 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 3855)
  covalent geometry    : angle       0.57766 /  0.29 ( 5180)
  hydrogen bonds       : bond        0.03469 /  2.24 (  289)
  hydrogen bonds       : angle       3.81377 /  2.80 (  867)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.6959 (m-10) cc_final: 0.6654 (m-10)
REVERT: A  167 GLN cc_start: 0.7949 (mp10) cc_final: 0.7682 (mp10)
REVERT: A  230 LYS cc_start: 0.8350 (tttt) cc_final: 0.7851 (ttpt)
REVERT: A  233 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7855 (mmtp)
REVERT: A  294 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7751 (tm-30)
REVERT: A  296 SER cc_start: 0.5854 (OUTLIER) cc_final: 0.5053 (p)
REVERT: A  344 ASN cc_start: 0.7616 (t0) cc_final: 0.7228 (t0)
REVERT: A  378 MET cc_start: 0.7685 (tpp) cc_final: 0.7469 (tpt)
REVERT: A  462 MET cc_start: 0.7041 (mmm) cc_final: 0.6794 (mmm)
REVERT: A  549 GLU cc_start: 0.6347 (tm-30) cc_final: 0.5533 (tm-30)
REVERT: A  561 MET cc_start: 0.7347 (tpp) cc_final: 0.7146 (mmm)
REVERT: A  604 LYS cc_start: 0.8053 (mttt) cc_final: 0.7434 (mptt)
  outliers start: 14
  outliers final: 11
  residues processed: 120
  average time/residue: 0.0475
  time to fit residues: 6.9929
Evaluate side-chains
  121 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  538 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    0.4980
   chunk 26 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0570
   chunk 10 optimal weight:    0.2980
   chunk 21 optimal weight:    0.3980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.3698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.140855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.126199 restraints weight = 7294.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.129993 restraints weight = 3822.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.132563 restraints weight = 2306.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.134233 restraints weight = 1511.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.135543 restraints weight = 1071.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3855  Z= 0.136
  Angle     :  0.582   9.898   5180  Z= 0.296
  Chirality :  0.039   0.157    559
  Planarity :  0.003   0.033    678
  Dihedral  :  4.028  25.032    512
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 34.33 %
    Favored  : 62.94 %
  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:  2.42 (0.38), residues: 472
  helix:  2.06 (0.25), residues: 402
  sheet:  None (None), residues: 0
  loop : -1.17 (0.71), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 192 
 TYR   0.010   0.001   TYR A 482 
 PHE   0.008   0.001   PHE A 338 
 TRP   0.003   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 592 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.14 ( 3855)
  covalent geometry    : angle       0.58172 /  0.30 ( 5180)
  hydrogen bonds       : bond        0.03436 /  2.23 (  289)
  hydrogen bonds       : angle       3.82259 /  2.80 (  867)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.6957 (m-10) cc_final: 0.6675 (m-10)
REVERT: A  167 GLN cc_start: 0.7954 (mp10) cc_final: 0.7677 (mp10)
REVERT: A  230 LYS cc_start: 0.8342 (tttt) cc_final: 0.7786 (ttpt)
REVERT: A  233 LYS cc_start: 0.8281 (mmtm) cc_final: 0.7909 (mmtm)
REVERT: A  296 SER cc_start: 0.5769 (OUTLIER) cc_final: 0.5158 (p)
REVERT: A  344 ASN cc_start: 0.7666 (t0) cc_final: 0.7277 (t0)
REVERT: A  378 MET cc_start: 0.7722 (tpp) cc_final: 0.7507 (tpt)
REVERT: A  462 MET cc_start: 0.6957 (mmm) cc_final: 0.6728 (mmm)
REVERT: A  549 GLU cc_start: 0.6337 (tm-30) cc_final: 0.5528 (tm-30)
REVERT: A  561 MET cc_start: 0.7184 (tpp) cc_final: 0.6715 (tpp)
REVERT: A  604 LYS cc_start: 0.8053 (mttt) cc_final: 0.7474 (mptt)
  outliers start: 11
  outliers final: 9
  residues processed: 118
  average time/residue: 0.0501
  time to fit residues: 7.2392
Evaluate side-chains
  121 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  538 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 592 HIS
A 594 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.138601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.123884 restraints weight = 7273.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.127663 restraints weight = 3858.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.130183 restraints weight = 2343.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.131929 restraints weight = 1554.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.133214 restraints weight = 1102.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3855  Z= 0.202
  Angle     :  0.641  10.141   5180  Z= 0.328
  Chirality :  0.041   0.170    559
  Planarity :  0.003   0.041    678
  Dihedral  :  4.229  26.220    512
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 33.58 %
    Favored  : 63.18 %
  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:  2.11 (0.38), residues: 472
  helix:  1.85 (0.25), residues: 405
  sheet:  None (None), residues: 0
  loop : -1.35 (0.69), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 192 
 TYR   0.015   0.002   TYR A 482 
 PHE   0.008   0.001   PHE A 256 
 TRP   0.003   0.001   TRP A 169 
 HIS   0.006   0.001   HIS A 592 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00429 /  0.20 ( 3855)
  covalent geometry    : angle       0.64091 /  0.33 ( 5180)
  hydrogen bonds       : bond        0.03848 /  2.49 (  289)
  hydrogen bonds       : angle       4.06217 /  2.97 (  867)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.7002 (m-10) cc_final: 0.6705 (m-10)
REVERT: A  167 GLN cc_start: 0.8045 (mp10) cc_final: 0.7783 (mp10)
REVERT: A  230 LYS cc_start: 0.8358 (tttt) cc_final: 0.7801 (ttpt)
REVERT: A  233 LYS cc_start: 0.8303 (mmtm) cc_final: 0.7936 (mmtm)
REVERT: A  296 SER cc_start: 0.6016 (OUTLIER) cc_final: 0.5443 (m)
REVERT: A  344 ASN cc_start: 0.7768 (t0) cc_final: 0.7385 (t0)
REVERT: A  430 LEU cc_start: 0.6464 (tp) cc_final: 0.6004 (tp)
REVERT: A  462 MET cc_start: 0.6965 (mmm) cc_final: 0.6717 (mmm)
REVERT: A  549 GLU cc_start: 0.6390 (tm-30) cc_final: 0.5606 (tm-30)
REVERT: A  555 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7309 (mm-30)
REVERT: A  604 LYS cc_start: 0.8090 (mttt) cc_final: 0.7771 (mtmt)
  outliers start: 13
  outliers final: 10
  residues processed: 120
  average time/residue: 0.0527
  time to fit residues: 7.7447
Evaluate side-chains
  122 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  592 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   chunk 6 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 592 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.139268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.124607 restraints weight = 7344.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.128439 restraints weight = 3839.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.130912 restraints weight = 2314.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.132695 restraints weight = 1536.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.133853 restraints weight = 1082.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3855  Z= 0.176
  Angle     :  0.674  10.313   5180  Z= 0.335
  Chirality :  0.041   0.167    559
  Planarity :  0.004   0.041    678
  Dihedral  :  4.228  26.313    512
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 34.08 %
    Favored  : 62.94 %
  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:  2.09 (0.38), residues: 472
  helix:  1.85 (0.25), residues: 404
  sheet:  None (None), residues: 0
  loop : -1.46 (0.69), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 474 
 TYR   0.016   0.001   TYR A 482 
 PHE   0.008   0.001   PHE A 568 
 TRP   0.002   0.001   TRP A 169 
 HIS   0.005   0.001   HIS A 592 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00381 /  0.18 ( 3855)
  covalent geometry    : angle       0.67364 /  0.33 ( 5180)
  hydrogen bonds       : bond        0.03771 /  2.44 (  289)
  hydrogen bonds       : angle       4.03239 /  2.95 (  867)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A  167 GLN cc_start: 0.8061 (mp10) cc_final: 0.7784 (mp10)
REVERT: A  230 LYS cc_start: 0.8362 (tttt) cc_final: 0.7812 (ttpt)
REVERT: A  233 LYS cc_start: 0.8300 (mmtm) cc_final: 0.7934 (mmtm)
REVERT: A  296 SER cc_start: 0.5932 (OUTLIER) cc_final: 0.5156 (p)
REVERT: A  344 ASN cc_start: 0.7755 (t0) cc_final: 0.7382 (t0)
REVERT: A  462 MET cc_start: 0.6933 (mmm) cc_final: 0.6700 (mmm)
REVERT: A  549 GLU cc_start: 0.6367 (tm-30) cc_final: 0.5593 (tm-30)
REVERT: A  555 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7344 (mm-30)
REVERT: A  604 LYS cc_start: 0.8100 (mttt) cc_final: 0.7522 (mptt)
  outliers start: 12
  outliers final: 11
  residues processed: 118
  average time/residue: 0.0466
  time to fit residues: 6.7304
Evaluate side-chains
  122 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  592 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 31 optimal weight:    0.3980
   chunk 29 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0020
   chunk 25 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 8 optimal weight:    0.3980
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.4588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 592 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.140116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.125494 restraints weight = 7220.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.129253 restraints weight = 3811.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.131763 restraints weight = 2305.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.133534 restraints weight = 1536.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.134700 restraints weight = 1083.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3855  Z= 0.155
  Angle     :  0.673  10.418   5180  Z= 0.331
  Chirality :  0.040   0.165    559
  Planarity :  0.003   0.034    678
  Dihedral  :  4.156  26.208    512
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 33.83 %
    Favored  : 62.94 %
  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:  2.24 (0.38), residues: 472
  helix:  1.96 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -1.27 (0.69), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 474 
 TYR   0.014   0.001   TYR A 482 
 PHE   0.008   0.001   PHE A 338 
 TRP   0.002   0.001   TRP A 169 
 HIS   0.006   0.001   HIS A 592 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.15 ( 3855)
  covalent geometry    : angle       0.67267 /  0.33 ( 5180)
  hydrogen bonds       : bond        0.03622 /  2.32 (  289)
  hydrogen bonds       : angle       3.93386 /  2.88 (  867)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 666.03 seconds
wall clock time: 12 minutes 9.37 seconds (729.37 seconds total)