Starting phenix.real_space_refine
on Tue Mar  3 12:28:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p14_13155/03_2026/7p14_13155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p14_13155/03_2026/7p14_13155.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p14_13155/03_2026/7p14_13155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p14_13155/03_2026/7p14_13155.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p14_13155/03_2026/7p14_13155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p14_13155/03_2026/7p14_13155.cif"
  }
  resolution = 3.66
  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=   0.002 sd=   0.046
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      25      5.16       5
     C    2533      2.51       5
     N     579      2.21       5
     O     656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3796
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2706
          Classifications: {'peptide': 328}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 320}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 964
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 3, 'TRANS': 122}
    Chain: "A"
      Number of atoms: 126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 126
          Unusual residues: {'PLC': 2}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
  Time building chain proxies: 1.12, per 1000 atoms: 0.30
  Number of scatterers: 3796
  At special positions: 0
  Unit cell: (96.348, 69.006, 70.308, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     P       3     15.00
     O     656      8.00
     N     579      7.00
     C    2533      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  28 " - pdb=" SG  CYS B 102 " distance=2.03

  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: 0.29
  Conformation dependent library (CDL) restraints added in 177.9 milliseconds
  

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  846

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 2 sheets defined
      67.2% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 36
      removed outlier: 3.515A  pdb=" N   ILE A  15 " --> pdb=" O   SER A  11 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ILE A  16 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 67
      removed outlier: 3.741A  pdb=" N   VAL A  48 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 86
      removed outlier: 3.762A  pdb=" N   GLY A  86 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 82 through 86'
    Processing helix  chain 'A' and resid 87 through 105
      removed outlier: 3.530A  pdb=" N   PHE A  94 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 158
      removed outlier: 3.590A  pdb=" N   LEU A 134 " --> pdb=" O   ASP A 130 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   CYS A 144 " --> pdb=" O   TYR A 140 " (cutoff:3.500A)
      Proline residue:  A 145  - end of helix
      removed outlier: 3.572A  pdb=" N   LEU A 149 " --> pdb=" O   PRO A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 190
      removed outlier: 3.504A  pdb=" N   ARG A 187 " --> pdb=" O   GLN A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 197
      removed outlier: 5.032A  pdb=" N   LEU A 195 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG A 197 " --> pdb=" O   ASN A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 227
      removed outlier: 3.654A  pdb=" N   LEU A 206 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   VAL A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 250
      removed outlier: 3.535A  pdb=" N   VAL A 231 " --> pdb=" O   ASP A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 274
      removed outlier: 3.733A  pdb=" N   PHE A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL A 272 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   PHE A 273 " --> pdb=" O   PHE A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 281
      removed outlier: 4.233A  pdb=" N   GLN A 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 308
    Processing helix  chain 'A' and resid 314 through 343
      removed outlier: 3.616A  pdb=" N   ILE A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      Proline residue:  A 320  - end of helix
    Processing helix  chain 'B' and resid 93 through 97
    Processing helix  chain 'B' and resid 115 through 119
      removed outlier: 3.778A  pdb=" N   TYR B 119 " --> pdb=" O   VAL B 116 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 13
    Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 18
      removed outlier: 3.725A  pdb=" N   ALA B  55 " --> pdb=" O   TRP B  42 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ARG B  44 " --> pdb=" O   GLY B  53 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   GLY B  53 " --> pdb=" O   ARG B  44 " (cutoff:3.500A)

    256 hydrogen bonds defined for protein.
    735 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: 0.57

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 545
        1.32 -     1.44: 1168
        1.44 -     1.56: 2136
        1.56 -     1.69: 6
        1.69 -     1.81: 37
  Bond restraints: 3892
  Sorted by residual:
  bond pdb=" N   LYS A 284 "
       pdb=" CA  LYS A 284 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.29e-02 6.01e+03 1.05e+01
  bond pdb=" C20 P5S A 403 "
       pdb=" C21 P5S A 403 "
    ideal  model  delta    sigma   weight residual
    1.540  1.493  0.047 2.00e-02 2.50e+03 5.60e+00
  bond pdb=" C4  PLC A 402 "
       pdb=" O4P PLC A 402 "
    ideal  model  delta    sigma   weight residual
    1.409  1.456 -0.047 2.00e-02 2.50e+03 5.48e+00
  bond pdb=" C4  PLC A 401 "
       pdb=" O4P PLC A 401 "
    ideal  model  delta    sigma   weight residual
    1.409  1.454 -0.045 2.00e-02 2.50e+03 4.97e+00
  bond pdb=" C1  PLC A 402 "
       pdb=" O3P PLC A 402 "
    ideal  model  delta    sigma   weight residual
    1.410  1.453 -0.043 2.00e-02 2.50e+03 4.69e+00
  ... (remaining 3887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 5181
        2.12 -     4.23: 75
        4.23 -     6.35: 10
        6.35 -     8.47: 2
        8.47 -    10.58: 2
  Bond angle restraints: 5270
  Sorted by residual:
  angle pdb=" O3P PLC A 402 "
        pdb=" P   PLC A 402 "
        pdb=" O4P PLC A 402 "
      ideal   model   delta    sigma   weight residual
      93.62  104.20  -10.58 3.00e+00 1.11e-01 1.24e+01
  angle pdb=" O3P PLC A 401 "
        pdb=" P   PLC A 401 "
        pdb=" O4P PLC A 401 "
      ideal   model   delta    sigma   weight residual
      93.62  103.08   -9.46 3.00e+00 1.11e-01 9.94e+00
  angle pdb=" C3  PLC A 401 "
        pdb=" C2  PLC A 401 "
        pdb=" O2  PLC A 401 "
      ideal   model   delta    sigma   weight residual
     107.38  114.66   -7.28 3.00e+00 1.11e-01 5.89e+00
  angle pdb=" CA  LYS A 284 "
        pdb=" CB  LYS A 284 "
        pdb=" CG  LYS A 284 "
      ideal   model   delta    sigma   weight residual
     114.10  118.68   -4.58 2.00e+00 2.50e-01 5.24e+00
  angle pdb=" CA  LEU A 330 "
        pdb=" CB  LEU A 330 "
        pdb=" CG  LEU A 330 "
      ideal   model   delta    sigma   weight residual
     116.30  122.98   -6.68 3.50e+00 8.16e-02 3.65e+00
  ... (remaining 5265 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.26: 2099
       27.26 -    54.52: 136
       54.52 -    81.77: 21
       81.77 -   109.03: 8
      109.03 -   136.29: 3
  Dihedral angle restraints: 2267
    sinusoidal: 938
      harmonic: 1329
  Sorted by residual:
  dihedral pdb=" O2  PLC A 401 "
           pdb=" C1  PLC A 401 "
           pdb=" C2  PLC A 401 "
           pdb=" O3P PLC A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     304.29  168.00  136.29     1      3.00e+01 1.11e-03 1.84e+01
  dihedral pdb=" C3  PLC A 401 "
           pdb=" C1  PLC A 401 "
           pdb=" C2  PLC A 401 "
           pdb=" O3P PLC A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      67.16  -58.95  126.11     1      3.00e+01 1.11e-03 1.70e+01
  dihedral pdb=" C21 P5S A 403 "
           pdb=" C22 P5S A 403 "
           pdb=" C23 P5S A 403 "
           pdb=" C24 P5S A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.37  174.71  120.66     1      3.00e+01 1.11e-03 1.61e+01
  ... (remaining 2264 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 507
       0.053 -    0.106: 73
       0.106 -    0.159: 5
       0.159 -    0.213: 0
       0.213 -    0.266: 2
  Chirality restraints: 587
  Sorted by residual:
  chirality pdb=" C2  PLC A 401 "
            pdb=" C1  PLC A 401 "
            pdb=" C3  PLC A 401 "
            pdb=" O2  PLC A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -2.05   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" C2  P5S A 403 "
            pdb=" C1  P5S A 403 "
            pdb=" C3  P5S A 403 "
            pdb=" O37 P5S A 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.33    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  PRO A 201 "
            pdb=" N   PRO A 201 "
            pdb=" C   PRO A 201 "
            pdb=" CB  PRO A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.61e-01
  ... (remaining 584 not shown)

  Planarity restraints: 624
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 319 "    0.042 5.00e-02 4.00e+02   6.37e-02 6.49e+00
        pdb=" N   PRO A 320 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 320 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 320 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 200 "    0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO A 201 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 201 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 201 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  33 "   -0.005 2.00e-02 2.50e+03   9.48e-03 8.99e-01
        pdb=" C   ASN B  33 "    0.016 2.00e-02 2.50e+03
        pdb=" O   ASN B  33 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   ILE B  34 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 621 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1090
        2.82 -     3.34: 3666
        3.34 -     3.86: 5942
        3.86 -     4.38: 7105
        4.38 -     4.90: 12065
  Nonbonded interactions: 29868
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 260 "
            pdb=" NH2 ARG A 264 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   ILE A  16 "
            pdb=" OG1 THR A  20 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" OH  TYR A 182 "
            pdb=" O   LEU A 371 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" O   ILE A 175 "
            pdb=" OG1 THR A 179 "
     model   vdw
     2.393 3.040
  nonbonded pdb=" OH  TYR A 208 "
            pdb=" OH  TYR A 291 "
     model   vdw
     2.419 3.040
  ... (remaining 29863 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             0.560
  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:             0.020
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.410
  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:1.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
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   0.047   3893  Z= 0.220
  Angle     :  0.627  10.583   5272  Z= 0.286
  Chirality :  0.039   0.266    587
  Planarity :  0.004   0.064    624
  Dihedral  : 19.089 136.288   1418
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.11 (0.40), residues: 444
  helix:  1.37 (0.31), residues: 257
  sheet:  1.11 (0.70), residues: 52
  loop : -0.55 (0.57), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  51 
 TYR   0.015   0.001   TYR A 340 
 PHE   0.005   0.001   PHE A 225 
 TRP   0.005   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 3892)
  covalent geometry    : angle       0.62693 ( 5270)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       0.41090 (    2)
  hydrogen bonds       : bond        0.24301 (  256)
  hydrogen bonds       : angle       7.43826 (  735)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  139 THR cc_start: 0.9153 (m) cc_final: 0.8884 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0619
  time to fit residues: 5.7216
Evaluate side-chains
  63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** A 183 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 = 0.3810 r_free = 0.3810 target = 0.166213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.134251 restraints weight = 4392.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.137687 restraints weight = 2908.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.140131 restraints weight = 2203.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.141652 restraints weight = 1831.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.142515 restraints weight = 1624.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3893  Z= 0.146
  Angle     :  0.603   9.719   5272  Z= 0.298
  Chirality :  0.039   0.143    587
  Planarity :  0.004   0.039    624
  Dihedral  : 18.301 129.435    623
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  7.30 %
    Favored  : 91.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.39), residues: 444
  helix:  2.36 (0.29), residues: 265
  sheet:  0.34 (0.69), residues: 57
  loop : -0.41 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.015   0.001   TYR A 291 
 PHE   0.034   0.002   PHE A  94 
 TRP   0.008   0.001   TRP A  93 
 HIS   0.002   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 3892)
  covalent geometry    : angle       0.60275 ( 5270)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.14282 (    2)
  hydrogen bonds       : bond        0.04754 (  256)
  hydrogen bonds       : angle       4.38194 (  735)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   50 CYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7493 (m)
REVERT: A  130 ASP cc_start: 0.8942 (t0) cc_final: 0.8716 (t70)
REVERT: A  139 THR cc_start: 0.9123 (m) cc_final: 0.8808 (p)
REVERT: A  252 GLN cc_start: 0.8280 (pm20) cc_final: 0.8043 (pt0)
REVERT: B  127 GLN cc_start: 0.8475 (tp40) cc_final: 0.8212 (tp-100)
  outliers start: 4
  outliers final: 1
  residues processed: 73
  average time/residue: 0.0572
  time to fit residues: 5.4215
Evaluate side-chains
  68 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue   83 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
A 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.162894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.130150 restraints weight = 4408.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.133276 restraints weight = 2962.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.135876 restraints weight = 2286.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.137226 restraints weight = 1921.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.138372 restraints weight = 1718.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3893  Z= 0.182
  Angle     :  0.595   9.503   5272  Z= 0.295
  Chirality :  0.041   0.201    587
  Planarity :  0.003   0.038    624
  Dihedral  : 17.923 129.173    623
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  9.32 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.30 (0.39), residues: 444
  helix:  2.62 (0.29), residues: 265
  sheet:  0.93 (0.68), residues: 52
  loop : -0.63 (0.58), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.027   0.002   TYR A 343 
 PHE   0.020   0.001   PHE A 104 
 TRP   0.007   0.001   TRP A 177 
 HIS   0.001   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 3892)
  covalent geometry    : angle       0.59521 ( 5270)
  SS BOND              : bond        0.00099 (    1)
  SS BOND              : angle       0.28822 (    2)
  hydrogen bonds       : bond        0.04316 (  256)
  hydrogen bonds       : angle       4.17928 (  735)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A    7 ASN cc_start: 0.8903 (t0) cc_final: 0.8591 (m-40)
REVERT: A  130 ASP cc_start: 0.8995 (t0) cc_final: 0.8694 (t0)
REVERT: A  137 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8675 (m-10)
REVERT: A  232 LEU cc_start: 0.8465 (mp) cc_final: 0.8210 (mp)
REVERT: A  258 SER cc_start: 0.8899 (t) cc_final: 0.8602 (p)
REVERT: B  127 GLN cc_start: 0.8505 (tp40) cc_final: 0.8284 (tp-100)
  outliers start: 9
  outliers final: 5
  residues processed: 79
  average time/residue: 0.0509
  time to fit residues: 5.3086
Evaluate side-chains
  76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  137 PHE
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.167155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.135861 restraints weight = 4429.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.139198 restraints weight = 2986.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.141406 restraints weight = 2290.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.142725 restraints weight = 1915.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.144043 restraints weight = 1710.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3893  Z= 0.146
  Angle     :  0.553   8.774   5272  Z= 0.274
  Chirality :  0.039   0.194    587
  Planarity :  0.003   0.031    624
  Dihedral  : 17.325 126.942    623
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.84 %
    Favored  : 86.15 %
  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:  2.52 (0.40), residues: 444
  helix:  2.89 (0.29), residues: 264
  sheet:  0.83 (0.68), residues: 52
  loop : -0.65 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.015   0.001   TYR A 343 
 PHE   0.012   0.001   PHE A  94 
 TRP   0.007   0.001   TRP A 245 
 HIS   0.001   0.000   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3892)
  covalent geometry    : angle       0.55276 ( 5270)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.13641 (    2)
  hydrogen bonds       : bond        0.03719 (  256)
  hydrogen bonds       : angle       3.94004 (  735)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8891 (t0) cc_final: 0.8520 (t0)
REVERT: A  258 SER cc_start: 0.8895 (t) cc_final: 0.8649 (p)
REVERT: A  264 ARG cc_start: 0.7897 (ttm170) cc_final: 0.7548 (ttm170)
REVERT: B  127 GLN cc_start: 0.8309 (tp40) cc_final: 0.8058 (tp-100)
  outliers start: 8
  outliers final: 4
  residues processed: 74
  average time/residue: 0.0634
  time to fit residues: 5.9762
Evaluate side-chains
  70 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 23 optimal weight:    0.2980
   chunk 19 optimal weight:    0.2980
   chunk 18 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.171265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.140116 restraints weight = 4400.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.143238 restraints weight = 2951.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.145840 restraints weight = 2269.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.147152 restraints weight = 1897.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.148350 restraints weight = 1692.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3893  Z= 0.128
  Angle     :  0.540   8.375   5272  Z= 0.267
  Chirality :  0.039   0.198    587
  Planarity :  0.003   0.030    624
  Dihedral  : 16.867 125.789    623
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 12.34 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.64 (0.40), residues: 444
  helix:  3.02 (0.29), residues: 264
  sheet:  0.86 (0.67), residues: 52
  loop : -0.70 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 264 
 TYR   0.013   0.001   TYR A 343 
 PHE   0.020   0.001   PHE A   8 
 TRP   0.008   0.001   TRP A 245 
 HIS   0.001   0.000   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3892)
  covalent geometry    : angle       0.53989 ( 5270)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.20545 (    2)
  hydrogen bonds       : bond        0.03526 (  256)
  hydrogen bonds       : angle       3.81005 (  735)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8705 (t0) cc_final: 0.8309 (t0)
REVERT: A  199 PHE cc_start: 0.7780 (t80) cc_final: 0.7333 (t80)
REVERT: A  258 SER cc_start: 0.8829 (t) cc_final: 0.8609 (p)
REVERT: A  264 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7560 (ttm170)
REVERT: A  265 LEU cc_start: 0.8678 (tp) cc_final: 0.8421 (tt)
REVERT: B  127 GLN cc_start: 0.8363 (tp40) cc_final: 0.8127 (tp-100)
  outliers start: 8
  outliers final: 6
  residues processed: 73
  average time/residue: 0.0647
  time to fit residues: 6.0367
Evaluate side-chains
  71 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.165353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.134053 restraints weight = 4435.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.137349 restraints weight = 2996.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.139349 restraints weight = 2308.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.141018 restraints weight = 1953.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.141868 restraints weight = 1736.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3893  Z= 0.157
  Angle     :  0.564   8.480   5272  Z= 0.279
  Chirality :  0.040   0.206    587
  Planarity :  0.003   0.027    624
  Dihedral  : 16.836 125.641    623
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.60 %
    Favored  : 83.88 %
  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:  2.60 (0.40), residues: 444
  helix:  3.00 (0.29), residues: 263
  sheet:  0.84 (0.67), residues: 52
  loop : -0.71 (0.58), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.014   0.001   TYR A 343 
 PHE   0.014   0.001   PHE A 104 
 TRP   0.007   0.001   TRP A 245 
 HIS   0.001   0.000   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3892)
  covalent geometry    : angle       0.56378 ( 5270)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       0.21761 (    2)
  hydrogen bonds       : bond        0.03640 (  256)
  hydrogen bonds       : angle       3.85167 (  735)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8758 (t0) cc_final: 0.8342 (t0)
REVERT: A  199 PHE cc_start: 0.7858 (t80) cc_final: 0.7399 (t80)
REVERT: A  258 SER cc_start: 0.8846 (t) cc_final: 0.8642 (p)
REVERT: A  265 LEU cc_start: 0.8739 (tp) cc_final: 0.8482 (tt)
REVERT: B  127 GLN cc_start: 0.8379 (tp40) cc_final: 0.8122 (tp-100)
  outliers start: 10
  outliers final: 7
  residues processed: 75
  average time/residue: 0.0607
  time to fit residues: 5.8307
Evaluate side-chains
  73 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.168218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.136866 restraints weight = 4555.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.140304 restraints weight = 3054.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.142605 restraints weight = 2333.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.143962 restraints weight = 1950.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.144971 restraints weight = 1737.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3893  Z= 0.159
  Angle     :  0.561   8.263   5272  Z= 0.279
  Chirality :  0.040   0.211    587
  Planarity :  0.003   0.038    624
  Dihedral  : 16.737 125.383    623
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 14.11 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.54 (0.40), residues: 444
  helix:  2.94 (0.29), residues: 263
  sheet:  0.82 (0.66), residues: 52
  loop : -0.73 (0.58), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 264 
 TYR   0.014   0.001   TYR B 121 
 PHE   0.015   0.001   PHE A 104 
 TRP   0.006   0.001   TRP A 177 
 HIS   0.001   0.000   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 3892)
  covalent geometry    : angle       0.56066 ( 5270)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       0.21665 (    2)
  hydrogen bonds       : bond        0.03650 (  256)
  hydrogen bonds       : angle       3.84670 (  735)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8766 (t0) cc_final: 0.8346 (t0)
REVERT: A  199 PHE cc_start: 0.7875 (t80) cc_final: 0.7408 (t80)
REVERT: B  127 GLN cc_start: 0.8390 (tp40) cc_final: 0.8130 (tp-100)
  outliers start: 13
  outliers final: 8
  residues processed: 76
  average time/residue: 0.0533
  time to fit residues: 5.3224
Evaluate side-chains
  72 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.168513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.137227 restraints weight = 4493.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.140598 restraints weight = 3002.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.142602 restraints weight = 2299.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.144337 restraints weight = 1939.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.145243 restraints weight = 1720.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3893  Z= 0.146
  Angle     :  0.575   8.175   5272  Z= 0.288
  Chirality :  0.039   0.211    587
  Planarity :  0.003   0.054    624
  Dihedral  : 16.377 124.725    623
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.62 %
    Favored  : 80.86 %
  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:  2.48 (0.40), residues: 444
  helix:  2.89 (0.29), residues: 263
  sheet:  0.82 (0.66), residues: 52
  loop : -0.75 (0.58), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  97 
 TYR   0.031   0.001   TYR A 343 
 PHE   0.015   0.001   PHE A 104 
 TRP   0.017   0.001   TRP A  93 
 HIS   0.002   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3892)
  covalent geometry    : angle       0.57514 ( 5270)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.16859 (    2)
  hydrogen bonds       : bond        0.03585 (  256)
  hydrogen bonds       : angle       3.81767 (  735)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8712 (t0) cc_final: 0.8300 (t0)
REVERT: A  199 PHE cc_start: 0.7700 (t80) cc_final: 0.7197 (t80)
REVERT: A  259 MET cc_start: 0.7892 (tpp) cc_final: 0.7374 (tpp)
REVERT: B  127 GLN cc_start: 0.8390 (tp40) cc_final: 0.8128 (tp-100)
  outliers start: 10
  outliers final: 8
  residues processed: 74
  average time/residue: 0.0541
  time to fit residues: 5.3129
Evaluate side-chains
  74 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:    0.1980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.167401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.135662 restraints weight = 4491.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.139009 restraints weight = 2997.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.141068 restraints weight = 2295.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.142921 restraints weight = 1932.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.143419 restraints weight = 1711.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3893  Z= 0.138
  Angle     :  0.570   8.086   5272  Z= 0.283
  Chirality :  0.039   0.217    587
  Planarity :  0.003   0.023    624
  Dihedral  : 15.995 124.051    623
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.38 %
    Favored  : 80.10 %
  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:  2.50 (0.40), residues: 444
  helix:  2.97 (0.29), residues: 262
  sheet:  0.34 (0.65), residues: 57
  loop : -0.65 (0.58), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 264 
 TYR   0.022   0.001   TYR A 340 
 PHE   0.017   0.001   PHE A 104 
 TRP   0.016   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3892)
  covalent geometry    : angle       0.57028 ( 5270)
  SS BOND              : bond        0.00080 (    1)
  SS BOND              : angle       0.18149 (    2)
  hydrogen bonds       : bond        0.03525 (  256)
  hydrogen bonds       : angle       3.76610 (  735)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A    1 MET cc_start: 0.8078 (tmm) cc_final: 0.7769 (tmm)
REVERT: A  130 ASP cc_start: 0.8674 (t0) cc_final: 0.8224 (t0)
REVERT: A  199 PHE cc_start: 0.7688 (t80) cc_final: 0.7127 (t80)
REVERT: B  127 GLN cc_start: 0.8412 (tp40) cc_final: 0.8121 (tp-100)
  outliers start: 10
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0488
  time to fit residues: 4.8439
Evaluate side-chains
  76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

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 = 0.169624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.138418 restraints weight = 4491.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.141722 restraints weight = 2999.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.143806 restraints weight = 2304.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.145593 restraints weight = 1931.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.146301 restraints weight = 1718.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3893  Z= 0.158
  Angle     :  0.591   8.279   5272  Z= 0.296
  Chirality :  0.040   0.221    587
  Planarity :  0.003   0.030    624
  Dihedral  : 15.851 124.009    623
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.63 %
    Favored  : 80.10 %
  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:  2.39 (0.40), residues: 444
  helix:  2.85 (0.29), residues: 262
  sheet:  0.33 (0.65), residues: 57
  loop : -0.64 (0.59), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 264 
 TYR   0.038   0.002   TYR A 340 
 PHE   0.017   0.001   PHE A 104 
 TRP   0.009   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 3892)
  covalent geometry    : angle       0.59143 ( 5270)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.19682 (    2)
  hydrogen bonds       : bond        0.03659 (  256)
  hydrogen bonds       : angle       3.85181 (  735)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A    1 MET cc_start: 0.8012 (tmm) cc_final: 0.7723 (tmm)
REVERT: A  130 ASP cc_start: 0.8689 (t0) cc_final: 0.8271 (t0)
REVERT: A  199 PHE cc_start: 0.7641 (t80) cc_final: 0.7110 (t80)
REVERT: B  127 GLN cc_start: 0.8406 (tp40) cc_final: 0.8122 (tp-100)
  outliers start: 9
  outliers final: 9
  residues processed: 70
  average time/residue: 0.0500
  time to fit residues: 4.6693
Evaluate side-chains
  72 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  208 TYR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.169409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.138194 restraints weight = 4462.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.141586 restraints weight = 3001.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.143601 restraints weight = 2289.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.145331 restraints weight = 1930.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.146574 restraints weight = 1707.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3893  Z= 0.152
  Angle     :  0.584   8.326   5272  Z= 0.293
  Chirality :  0.040   0.221    587
  Planarity :  0.003   0.032    624
  Dihedral  : 15.619 123.848    623
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.13 %
    Favored  : 80.35 %
  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:  2.38 (0.40), residues: 444
  helix:  2.83 (0.29), residues: 262
  sheet:  0.34 (0.65), residues: 57
  loop : -0.63 (0.58), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 264 
 TYR   0.037   0.001   TYR A 340 
 PHE   0.017   0.001   PHE A 104 
 TRP   0.009   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3892)
  covalent geometry    : angle       0.58383 ( 5270)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.19975 (    2)
  hydrogen bonds       : bond        0.03694 (  256)
  hydrogen bonds       : angle       3.88114 (  735)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 740.70 seconds
wall clock time: 13 minutes 26.10 seconds (806.10 seconds total)