Starting phenix.real_space_refine
on Thu Sep 10 20:48:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/23ic_68988/09_2026/23ic_68988.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/23ic_68988/09_2026/23ic_68988.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/23ic_68988/09_2026/23ic_68988.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/23ic_68988/09_2026/23ic_68988.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/23ic_68988/09_2026/23ic_68988.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/23ic_68988/09_2026/23ic_68988.cif"
  }
  resolution = 3.5
  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=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2146      2.51       5
     N     510      2.21       5
     O     553      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3229
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3229
          Classifications: {'peptide': 425}
          Link IDs: {'PTRANS': 15, 'TRANS': 409}
          Chain breaks: 4
  Time building chain proxies: 0.76, per 1000 atoms: 0.24
  Number of scatterers: 3229
  At special positions: 0
  Unit cell: (74.8, 68, 77.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     553      8.00
     N     510      7.00
     C    2146      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: 0.27
  Conformation dependent library (CDL) restraints added in 123.7 milliseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  760

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 0 sheets defined
      82.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 47
    Processing helix  chain 'A' and resid 47 through 57
      removed outlier: 3.579A  pdb=" N   ILE A  51 " --> pdb=" O   LYS A  47 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS A  53 " --> pdb=" O   PRO A  49 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   SER A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   VAL A  55 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 85
      removed outlier: 3.515A  pdb=" N   THR A  85 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 81 through 85'
    Processing helix  chain 'A' and resid 87 through 117
      removed outlier: 3.715A  pdb=" N   GLY A  93 " --> pdb=" O   SER A  89 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   PHE A 108 " --> pdb=" O   SER A 104 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   PHE A 109 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASP A 115 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ARG A 116 " --> pdb=" O   HIS A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 139
    Processing helix  chain 'A' and resid 147 through 163
      removed outlier: 3.625A  pdb=" N   PHE A 151 " --> pdb=" O   ASN A 147 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ILE A 154 " --> pdb=" O   TYR A 150 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN A 155 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 176
      removed outlier: 3.625A  pdb=" N   SER A 168 " --> pdb=" O   ILE A 164 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   TRP A 176 " --> pdb=" O   ILE A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 190
    Processing helix  chain 'A' and resid 191 through 209
      removed outlier: 4.205A  pdb=" N   LYS A 209 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 234
      Proline residue:  A 219  - end of helix
    Processing helix  chain 'A' and resid 283 through 311
      Proline residue:  A 306  - end of helix
    Processing helix  chain 'A' and resid 313 through 317
      removed outlier: 3.973A  pdb=" N   GLY A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLU A 317 " --> pdb=" O   ILE A 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 317'
    Processing helix  chain 'A' and resid 320 through 350
      removed outlier: 4.806A  pdb=" N   SER A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   THR A 329 " --> pdb=" O   GLY A 325 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ILE A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 375
      removed outlier: 3.889A  pdb=" N   THR A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ILE A 364 " --> pdb=" O   MET A 360 " (cutoff:3.500A)
      Proline residue:  A 365  - end of helix
      removed outlier: 4.725A  pdb=" N   SER A 375 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 409
      Proline residue:  A 395  - end of helix
      removed outlier: 3.666A  pdb=" N   VAL A 403 " --> pdb=" O   ILE A 399 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   SER A 404 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 414
    Processing helix  chain 'A' and resid 419 through 443
      Proline residue:  A 439  - end of helix
    Processing helix  chain 'A' and resid 452 through 467
    Processing helix  chain 'A' and resid 468 through 478

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

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 641
        1.33 -     1.45: 843
        1.45 -     1.57: 1799
        1.57 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 3318
  Sorted by residual:
  bond pdb=" N   SER A 451 "
       pdb=" CA  SER A 451 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.18e-02 7.18e+03 6.91e+00
  bond pdb=" N   LEU A 207 "
       pdb=" CA  LEU A 207 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.28e-02 6.10e+03 5.68e+00
  bond pdb=" N   SER A 448 "
       pdb=" CA  SER A 448 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.33e-02 5.65e+03 5.68e+00
  bond pdb=" N   SER A 446 "
       pdb=" CA  SER A 446 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.029 1.22e-02 6.72e+03 5.65e+00
  bond pdb=" N   LEU A 208 "
       pdb=" CA  LEU A 208 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.52e+00
  ... (remaining 3313 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 4334
        1.71 -     3.42: 156
        3.42 -     5.13: 21
        5.13 -     6.83: 7
        6.83 -     8.54: 1
  Bond angle restraints: 4519
  Sorted by residual:
  angle pdb=" N   SER A 451 "
        pdb=" CA  SER A 451 "
        pdb=" C   SER A 451 "
      ideal   model   delta    sigma   weight residual
     112.72  108.17    4.55 1.14e+00 7.69e-01 1.59e+01
  angle pdb=" C   TRP A  80 "
        pdb=" N   LEU A  81 "
        pdb=" CA  LEU A  81 "
      ideal   model   delta    sigma   weight residual
     121.62  127.50   -5.88 1.57e+00 4.06e-01 1.40e+01
  angle pdb=" CA  GLY A 211 "
        pdb=" C   GLY A 211 "
        pdb=" O   GLY A 211 "
      ideal   model   delta    sigma   weight residual
     121.49  118.01    3.48 9.60e-01 1.09e+00 1.32e+01
  angle pdb=" CA  GLY A 211 "
        pdb=" C   GLY A 211 "
        pdb=" N   TRP A 212 "
      ideal   model   delta    sigma   weight residual
     114.58  117.63   -3.05 8.60e-01 1.35e+00 1.26e+01
  angle pdb=" CA  THR A  72 "
        pdb=" C   THR A  72 "
        pdb=" O   THR A  72 "
      ideal   model   delta    sigma   weight residual
     122.27  118.26    4.01 1.16e+00 7.43e-01 1.20e+01
  ... (remaining 4514 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.77: 1574
       12.77 -    25.55: 198
       25.55 -    38.32: 75
       38.32 -    51.10: 7
       51.10 -    63.87: 4
  Dihedral angle restraints: 1858
    sinusoidal: 663
      harmonic: 1195
  Sorted by residual:
  dihedral pdb=" CA  VAL A 232 "
           pdb=" C   VAL A 232 "
           pdb=" N   PHE A 233 "
           pdb=" CA  PHE A 233 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.60  -15.40     0      5.00e+00 4.00e-02 9.49e+00
  dihedral pdb=" CA  TYR A  39 "
           pdb=" C   TYR A  39 "
           pdb=" N   THR A  40 "
           pdb=" CA  THR A  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.04   14.96     0      5.00e+00 4.00e-02 8.95e+00
  dihedral pdb=" CA  ILE A 164 "
           pdb=" C   ILE A 164 "
           pdb=" N   GLY A 165 "
           pdb=" CA  GLY A 165 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.49  -14.51     0      5.00e+00 4.00e-02 8.42e+00
  ... (remaining 1855 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 309
       0.030 -    0.060: 126
       0.060 -    0.090: 65
       0.090 -    0.120: 20
       0.120 -    0.150: 7
  Chirality restraints: 527
  Sorted by residual:
  chirality pdb=" CA  LEU A  81 "
            pdb=" N   LEU A  81 "
            pdb=" C   LEU A  81 "
            pdb=" CB  LEU A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  ILE A 281 "
            pdb=" N   ILE A 281 "
            pdb=" C   ILE A 281 "
            pdb=" CB  ILE A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.13e-01
  chirality pdb=" CA  PRO A  82 "
            pdb=" N   PRO A  82 "
            pdb=" C   PRO A  82 "
            pdb=" CB  PRO A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.14e-01
  ... (remaining 524 not shown)

  Planarity restraints: 546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 439 "   -0.009 2.00e-02 2.50e+03   1.84e-02 3.37e+00
        pdb=" C   PRO A 439 "    0.032 2.00e-02 2.50e+03
        pdb=" O   PRO A 439 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 440 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 237 "    0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO A 238 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 238 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 238 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 206 "    0.007 2.00e-02 2.50e+03   1.35e-02 1.82e+00
        pdb=" C   PHE A 206 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   PHE A 206 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU A 207 "    0.008 2.00e-02 2.50e+03
  ... (remaining 543 not shown)

  Histogram of nonbonded interaction distances:
        2.57 -     3.04: 2017
        3.04 -     3.50: 3616
        3.50 -     3.97: 5075
        3.97 -     4.43: 6090
        4.43 -     4.90: 9621
  Nonbonded interactions: 26419
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 452 "
            pdb=" N   THR A 455 "
     model   vdw
     2.572 3.120
  nonbonded pdb=" O   HIS A  71 "
            pdb=" C   THR A  72 "
     model   vdw
     2.583 3.270
  nonbonded pdb=" O   THR A  72 "
            pdb=" OG1 THR A  72 "
     model   vdw
     2.583 3.040
  nonbonded pdb=" O   ALA A 452 "
            pdb=" C   VAL A 453 "
     model   vdw
     2.647 3.270
  nonbonded pdb=" N   TRP A 450 "
            pdb=" O   TRP A 450 "
     model   vdw
     2.648 2.496
  ... (remaining 26414 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:             4.190
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.540
  Find NCS groups from input model:        0.030
  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:1.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
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   0.037   3318  Z= 0.271
  Angle     :  0.705   8.543   4519  Z= 0.413
  Chirality :  0.044   0.150    527
  Planarity :  0.005   0.038    546
  Dihedral  : 12.833  63.871   1098
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  1.19 %
    Favored  : 98.22 %
  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:  0.66 (0.41), residues: 415
  helix:  1.26 (0.29), residues: 307
  sheet:  None (None), residues: 0
  loop : -1.99 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 352 
 TYR   0.020   0.001   TYR A  39 
 PHE   0.019   0.002   PHE A 292 
 TRP   0.008   0.001   TRP A 212 
 HIS   0.006   0.001   HIS A 192 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.27 ( 3318)
  covalent geometry    : angle       0.70479 /  0.41 ( 4519)
  hydrogen bonds       : bond        0.13403 /  8.84 (  235)
  hydrogen bonds       : angle       5.92040 /  4.26 (  699)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  379 MET cc_start: 0.6580 (tmm) cc_final: 0.6318 (tmm)
REVERT: A  383 CYS cc_start: 0.8997 (m) cc_final: 0.8396 (m)
REVERT: A  385 MET cc_start: 0.8628 (tpp) cc_final: 0.8184 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0599
  time to fit residues: 8.4998
Evaluate side-chains
  83 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.1980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 112 HIS
A 175 ASN
A 344 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.140132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.124374 restraints weight = 5809.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.128102 restraints weight = 2624.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.130545 restraints weight = 1524.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.132045 restraints weight = 1043.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.133186 restraints weight = 807.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3318  Z= 0.140
  Angle     :  0.606   8.850   4519  Z= 0.298
  Chirality :  0.041   0.162    527
  Planarity :  0.004   0.036    546
  Dihedral  :  3.665  13.882    444
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.84 %
    Favored  : 82.49 %
  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:  1.73 (0.42), residues: 415
  helix:  2.04 (0.29), residues: 311
  sheet:  None (None), residues: 0
  loop : -1.72 (0.60), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 352 
 TYR   0.015   0.001   TYR A 103 
 PHE   0.015   0.001   PHE A 292 
 TRP   0.015   0.001   TRP A 212 
 HIS   0.010   0.002   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.14 ( 3318)
  covalent geometry    : angle       0.60557 /  0.30 ( 4519)
  hydrogen bonds       : bond        0.04073 /  2.66 (  235)
  hydrogen bonds       : angle       4.54638 /  3.14 (  699)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   61 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7448 (mmmm)
REVERT: A  344 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7553 (t-90)
REVERT: A  383 CYS cc_start: 0.9074 (m) cc_final: 0.8468 (m)
  outliers start: 9
  outliers final: 4
  residues processed: 89
  average time/residue: 0.0573
  time to fit residues: 6.3211
Evaluate side-chains
  86 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  344 HIS
Chi-restraints excluded: chain A residue  466 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 112 HIS
A 175 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.135267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.119240 restraints weight = 5810.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.122779 restraints weight = 2662.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.125174 restraints weight = 1577.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.126769 restraints weight = 1094.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.127428 restraints weight = 847.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3318  Z= 0.161
  Angle     :  0.611   9.324   4519  Z= 0.300
  Chirality :  0.041   0.136    527
  Planarity :  0.004   0.040    546
  Dihedral  :  3.769  14.139    444
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 16.62 %
    Favored  : 79.23 %
  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:  1.83 (0.43), residues: 415
  helix:  2.02 (0.29), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.45 (0.67), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 352 
 TYR   0.019   0.001   TYR A 103 
 PHE   0.017   0.002   PHE A 292 
 TRP   0.013   0.001   TRP A 212 
 HIS   0.007   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.16 ( 3318)
  covalent geometry    : angle       0.61110 /  0.30 ( 4519)
  hydrogen bonds       : bond        0.03931 /  2.55 (  235)
  hydrogen bonds       : angle       4.53314 /  3.10 (  699)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8515 (tt)
  outliers start: 14
  outliers final: 9
  residues processed: 89
  average time/residue: 0.0592
  time to fit residues: 6.6194
Evaluate side-chains
  88 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  117 MET
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  469 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0980
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0970
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  84 ASN
A 112 HIS
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.135673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.120819 restraints weight = 5748.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.124273 restraints weight = 2612.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.126491 restraints weight = 1514.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.127995 restraints weight = 1044.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.129016 restraints weight = 796.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3318  Z= 0.149
  Angle     :  0.591  10.218   4519  Z= 0.289
  Chirality :  0.040   0.138    527
  Planarity :  0.004   0.043    546
  Dihedral  :  3.785  14.650    444
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 19.88 %
    Favored  : 75.96 %
  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:  1.85 (0.43), residues: 415
  helix:  1.94 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.19 (0.70), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 116 
 TYR   0.017   0.001   TYR A 103 
 PHE   0.017   0.001   PHE A 292 
 TRP   0.012   0.001   TRP A 212 
 HIS   0.006   0.001   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.15 ( 3318)
  covalent geometry    : angle       0.59137 /  0.29 ( 4519)
  hydrogen bonds       : bond        0.03893 /  2.54 (  235)
  hydrogen bonds       : angle       4.45360 /  3.06 (  699)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8246 (mm)
REVERT: A  349 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8528 (tt)
  outliers start: 14
  outliers final: 7
  residues processed: 89
  average time/residue: 0.0624
  time to fit residues: 6.9382
Evaluate side-chains
  89 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  469 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0770
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.5938

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 112 HIS
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 GLN
A 175 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.131862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.116147 restraints weight = 5872.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.119755 restraints weight = 2692.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.121826 restraints weight = 1575.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.123510 restraints weight = 1118.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.124527 restraints weight = 862.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3318  Z= 0.150
  Angle     :  0.607   9.950   4519  Z= 0.297
  Chirality :  0.041   0.197    527
  Planarity :  0.004   0.045    546
  Dihedral  :  3.812  14.880    444
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 20.18 %
    Favored  : 74.78 %
  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:  1.87 (0.43), residues: 415
  helix:  1.93 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.11 (0.71), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 371 
 TYR   0.016   0.001   TYR A 103 
 PHE   0.017   0.001   PHE A 292 
 TRP   0.011   0.001   TRP A 212 
 HIS   0.006   0.001   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.15 ( 3318)
  covalent geometry    : angle       0.60671 /  0.30 ( 4519)
  hydrogen bonds       : bond        0.03879 /  2.52 (  235)
  hydrogen bonds       : angle       4.46067 /  3.07 (  699)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8260 (mm)
REVERT: A  379 MET cc_start: 0.6652 (tmm) cc_final: 0.6432 (tmm)
REVERT: A  475 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8168 (mm-30)
  outliers start: 17
  outliers final: 13
  residues processed: 88
  average time/residue: 0.0564
  time to fit residues: 6.1987
Evaluate side-chains
  90 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  117 MET
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  469 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    0.0670
   chunk 14 optimal weight:    0.2980
   chunk 18 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 39 optimal weight:    0.0000
   chunk 20 optimal weight:    0.0470
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.1620

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 112 HIS
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.135868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.119429 restraints weight = 5821.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.123167 restraints weight = 2721.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.125568 restraints weight = 1613.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.127089 restraints weight = 1123.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.128229 restraints weight = 885.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3318  Z= 0.121
  Angle     :  0.628  11.000   4519  Z= 0.297
  Chirality :  0.039   0.155    527
  Planarity :  0.004   0.046    546
  Dihedral  :  3.768  15.210    444
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 21.36 %
    Favored  : 74.48 %
  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:  1.86 (0.42), residues: 415
  helix:  1.93 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.17 (0.69), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  46 
 TYR   0.016   0.001   TYR A 103 
 PHE   0.017   0.001   PHE A 292 
 TRP   0.010   0.001   TRP A 212 
 HIS   0.006   0.001   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 ( 3318)
  covalent geometry    : angle       0.62830 /  0.30 ( 4519)
  hydrogen bonds       : bond        0.03620 /  2.34 (  235)
  hydrogen bonds       : angle       4.36990 /  3.01 (  699)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8232 (mm)
  outliers start: 14
  outliers final: 11
  residues processed: 88
  average time/residue: 0.0485
  time to fit residues: 5.5132
Evaluate side-chains
  89 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  117 MET
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  469 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 112 HIS
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.131598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.115989 restraints weight = 6027.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.119565 restraints weight = 2725.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.121894 restraints weight = 1586.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.123357 restraints weight = 1094.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.124437 restraints weight = 854.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3318  Z= 0.160
  Angle     :  0.637  10.579   4519  Z= 0.305
  Chirality :  0.041   0.137    527
  Planarity :  0.004   0.046    546
  Dihedral  :  3.803  15.005    444
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 23.15 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.84 (0.42), residues: 415
  helix:  1.95 (0.29), residues: 313
  sheet:  None (None), residues: 0
  loop : -1.10 (0.68), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 116 
 TYR   0.016   0.001   TYR A 103 
 PHE   0.018   0.001   PHE A 292 
 TRP   0.010   0.001   TRP A 212 
 HIS   0.010   0.002   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.16 ( 3318)
  covalent geometry    : angle       0.63650 /  0.30 ( 4519)
  hydrogen bonds       : bond        0.03790 /  2.46 (  235)
  hydrogen bonds       : angle       4.45380 /  3.05 (  699)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8280 (mm)
REVERT: A  136 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8190 (tt)
REVERT: A  321 ASP cc_start: 0.8045 (m-30) cc_final: 0.7804 (m-30)
  outliers start: 13
  outliers final: 10
  residues processed: 85
  average time/residue: 0.0568
  time to fit residues: 6.1176
Evaluate side-chains
  88 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  117 MET
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  469 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0050
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.4594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 112 HIS
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 344 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.132291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.116871 restraints weight = 5960.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.120373 restraints weight = 2692.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.122693 restraints weight = 1572.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.124318 restraints weight = 1081.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.125354 restraints weight = 824.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3318  Z= 0.140
  Angle     :  0.649  10.830   4519  Z= 0.308
  Chirality :  0.040   0.139    527
  Planarity :  0.004   0.047    546
  Dihedral  :  3.852  15.086    444
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 22.85 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.83 (0.42), residues: 415
  helix:  1.93 (0.29), residues: 313
  sheet:  None (None), residues: 0
  loop : -1.06 (0.68), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  46 
 TYR   0.015   0.001   TYR A 103 
 PHE   0.018   0.001   PHE A 292 
 TRP   0.010   0.001   TRP A 212 
 HIS   0.005   0.001   HIS A  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 ( 3318)
  covalent geometry    : angle       0.64880 /  0.31 ( 4519)
  hydrogen bonds       : bond        0.03722 /  2.41 (  235)
  hydrogen bonds       : angle       4.44535 /  3.06 (  699)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8294 (mm)
REVERT: A  136 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8219 (tt)
REVERT: A  344 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7683 (t-90)
  outliers start: 16
  outliers final: 10
  residues processed: 89
  average time/residue: 0.0493
  time to fit residues: 5.7025
Evaluate side-chains
  89 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  117 MET
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  344 HIS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  469 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.0270
   chunk 24 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0970
   chunk 29 optimal weight:    0.0370
   chunk 34 optimal weight:    0.5980
   chunk 20 optimal weight:    0.1980
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0170
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.0752

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 112 HIS
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.136041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.120651 restraints weight = 5856.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.124112 restraints weight = 2688.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.126216 restraints weight = 1595.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.127967 restraints weight = 1133.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.128675 restraints weight = 866.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3318  Z= 0.127
  Angle     :  0.671  11.059   4519  Z= 0.315
  Chirality :  0.040   0.164    527
  Planarity :  0.004   0.047    546
  Dihedral  :  3.933  15.529    444
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 25.82 %
    Favored  : 71.22 %
  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:  1.86 (0.42), residues: 415
  helix:  1.97 (0.29), residues: 312
  sheet:  None (None), residues: 0
  loop : -1.11 (0.67), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 116 
 TYR   0.014   0.001   TYR A 103 
 PHE   0.017   0.001   PHE A 292 
 TRP   0.010   0.001   TRP A 212 
 HIS   0.006   0.002   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.13 ( 3318)
  covalent geometry    : angle       0.67107 /  0.31 ( 4519)
  hydrogen bonds       : bond        0.03610 /  2.36 (  235)
  hydrogen bonds       : angle       4.36587 /  3.01 (  699)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8212 (mm)
  outliers start: 10
  outliers final: 8
  residues processed: 86
  average time/residue: 0.0475
  time to fit residues: 5.2076
Evaluate side-chains
  89 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  117 MET
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  469 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 41 optimal weight:    0.4980
   chunk 2 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 112 HIS
** A 146 HIS ** 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 = 0.3713 r_free = 0.3713 target = 0.132307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.116456 restraints weight = 5926.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.119995 restraints weight = 2762.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.122309 restraints weight = 1639.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.123379 restraints weight = 1143.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.124624 restraints weight = 936.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3318  Z= 0.181
  Angle     :  0.728  10.818   4519  Z= 0.343
  Chirality :  0.043   0.203    527
  Planarity :  0.004   0.048    546
  Dihedral  :  4.051  15.317    444
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 25.82 %
    Favored  : 71.22 %
  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:  1.57 (0.42), residues: 415
  helix:  1.70 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.19 (0.68), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  69 
 TYR   0.015   0.002   TYR A 103 
 PHE   0.017   0.002   PHE A 292 
 TRP   0.009   0.001   TRP A 212 
 HIS   0.005   0.001   HIS A  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.18 ( 3318)
  covalent geometry    : angle       0.72849 /  0.34 ( 4519)
  hydrogen bonds       : bond        0.03951 /  2.53 (  235)
  hydrogen bonds       : angle       4.56818 /  3.14 (  699)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   92 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8272 (mm)
  outliers start: 10
  outliers final: 9
  residues processed: 84
  average time/residue: 0.0499
  time to fit residues: 5.3870
Evaluate side-chains
  87 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  117 MET
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  469 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0030
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.4990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 112 HIS
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.132826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.117160 restraints weight = 6025.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.120518 restraints weight = 2800.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.122891 restraints weight = 1690.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.124276 restraints weight = 1173.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.125421 restraints weight = 927.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3318  Z= 0.147
  Angle     :  0.718  11.147   4519  Z= 0.335
  Chirality :  0.042   0.217    527
  Planarity :  0.004   0.048    546
  Dihedral  :  4.114  15.567    444
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 25.82 %
    Favored  : 71.22 %
  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:  1.66 (0.42), residues: 415
  helix:  1.73 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.01 (0.69), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 116 
 TYR   0.015   0.001   TYR A 103 
 PHE   0.017   0.001   PHE A 292 
 TRP   0.010   0.001   TRP A 212 
 HIS   0.008   0.002   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 ( 3318)
  covalent geometry    : angle       0.71771 /  0.33 ( 4519)
  hydrogen bonds       : bond        0.03805 /  2.46 (  235)
  hydrogen bonds       : angle       4.53104 /  3.12 (  699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 800.20 seconds
wall clock time: 14 minutes 25.13 seconds (865.13 seconds total)