Starting phenix.real_space_refine
on Tue Mar  3 13:40:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f6v_31482/03_2026/7f6v_31482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f6v_31482/03_2026/7f6v_31482.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f6v_31482/03_2026/7f6v_31482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f6v_31482/03_2026/7f6v_31482.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f6v_31482/03_2026/7f6v_31482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f6v_31482/03_2026/7f6v_31482.map"
  }
  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=   0.001 sd=   0.048
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      30      5.16       5
     C    3526      2.51       5
     N     866      2.21       5
     O     892      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5314
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2629
          Classifications: {'peptide': 313}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 305}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 2629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2629
          Classifications: {'peptide': 313}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 305}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.20, per 1000 atoms: 0.23
  Number of scatterers: 5314
  At special positions: 0
  Unit cell: (94.302, 116.61, 92.274, 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      30     16.00
     O     892      8.00
     N     866      7.00
     C    3526      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 265.7 milliseconds
  

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1196

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      87.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 69
      removed outlier: 3.562A  pdb=" N   ARG A  34 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A  31 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   LYS A  36 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 99
    Processing helix  chain 'A' and resid 107 through 113
    Processing helix  chain 'A' and resid 122 through 154
    Processing helix  chain 'A' and resid 159 through 186
    Processing helix  chain 'A' and resid 192 through 210
      removed outlier: 3.758A  pdb=" N   TYR A 198 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 248
      removed outlier: 4.307A  pdb=" N   LYS A 218 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 299
      Proline residue:  A 277  - end of helix
    Processing helix  chain 'A' and resid 303 through 334
      Proline residue:  A 313  - end of helix
    Processing helix  chain 'B' and resid 9 through 69
      removed outlier: 3.562A  pdb=" N   ARG B  34 " --> pdb=" O   HIS B  30 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   LEU B  35 " --> pdb=" O   ARG B  31 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   LYS B  36 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 99
    Processing helix  chain 'B' and resid 107 through 113
    Processing helix  chain 'B' and resid 122 through 154
    Processing helix  chain 'B' and resid 159 through 186
    Processing helix  chain 'B' and resid 192 through 210
      removed outlier: 3.758A  pdb=" N   TYR B 198 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 248
      removed outlier: 4.307A  pdb=" N   LYS B 218 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 299
      Proline residue:  B 277  - end of helix
    Processing helix  chain 'B' and resid 303 through 334
      Proline residue:  B 313  - end of helix

    452 hydrogen bonds defined for protein.
    1356 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: 0.75

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1596
        1.34 -     1.46: 1356
        1.46 -     1.58: 2474
        1.58 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 5470
  Sorted by residual:
  bond pdb=" C10 CLR A 401 "
       pdb=" C9  CLR A 401 "
    ideal  model  delta    sigma   weight residual
    1.551  1.520  0.031 2.00e-02 2.50e+03 2.44e+00
  bond pdb=" C10 CLR B 401 "
       pdb=" C9  CLR B 401 "
    ideal  model  delta    sigma   weight residual
    1.551  1.520  0.031 2.00e-02 2.50e+03 2.43e+00
  bond pdb=" C5  CLR B 401 "
       pdb=" C6  CLR B 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.301  0.031 2.00e-02 2.50e+03 2.37e+00
  bond pdb=" C5  CLR A 401 "
       pdb=" C6  CLR A 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.301  0.031 2.00e-02 2.50e+03 2.35e+00
  bond pdb=" C13 CLR A 401 "
       pdb=" C17 CLR A 401 "
    ideal  model  delta    sigma   weight residual
    1.550  1.525  0.025 2.00e-02 2.50e+03 1.57e+00
  ... (remaining 5465 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 7161
        1.86 -     3.72: 191
        3.72 -     5.59: 40
        5.59 -     7.45: 8
        7.45 -     9.31: 4
  Bond angle restraints: 7404
  Sorted by residual:
  angle pdb=" C   CYS A  68 "
        pdb=" N   LYS A  69 "
        pdb=" CA  LYS A  69 "
      ideal   model   delta    sigma   weight residual
     119.78  123.78   -4.00 1.24e+00 6.50e-01 1.04e+01
  angle pdb=" C   CYS B  68 "
        pdb=" N   LYS B  69 "
        pdb=" CA  LYS B  69 "
      ideal   model   delta    sigma   weight residual
     119.78  123.78   -4.00 1.24e+00 6.50e-01 1.04e+01
  angle pdb=" C13 CLR A 401 "
        pdb=" C17 CLR A 401 "
        pdb=" C20 CLR A 401 "
      ideal   model   delta    sigma   weight residual
     119.60  110.29    9.31 3.00e+00 1.11e-01 9.64e+00
  angle pdb=" C13 CLR B 401 "
        pdb=" C17 CLR B 401 "
        pdb=" C20 CLR B 401 "
      ideal   model   delta    sigma   weight residual
     119.60  110.33    9.27 3.00e+00 1.11e-01 9.54e+00
  angle pdb=" C   LYS B  69 "
        pdb=" CA  LYS B  69 "
        pdb=" CB  LYS B  69 "
      ideal   model   delta    sigma   weight residual
     113.04  108.81    4.23 1.63e+00 3.76e-01 6.74e+00
  ... (remaining 7399 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 2954
       17.67 -    35.34: 262
       35.34 -    53.00: 42
       53.00 -    70.67: 8
       70.67 -    88.34: 4
  Dihedral angle restraints: 3270
    sinusoidal: 1422
      harmonic: 1848
  Sorted by residual:
  dihedral pdb=" CA  LEU B  32 "
           pdb=" C   LEU B  32 "
           pdb=" N   TYR B  33 "
           pdb=" CA  TYR B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.61  -16.39     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  LEU A  32 "
           pdb=" C   LEU A  32 "
           pdb=" N   TYR A  33 "
           pdb=" CA  TYR A  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.61  -16.39     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CB  GLU B 304 "
           pdb=" CG  GLU B 304 "
           pdb=" CD  GLU B 304 "
           pdb=" OE1 GLU B 304 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.34  -88.34     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 3267 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 772
       0.105 -    0.210: 18
       0.210 -    0.315: 2
       0.315 -    0.420: 2
       0.420 -    0.525: 2
  Chirality restraints: 796
  Sorted by residual:
  chirality pdb=" C14 CLR A 401 "
            pdb=" C13 CLR A 401 "
            pdb=" C15 CLR A 401 "
            pdb=" C8  CLR A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.84    0.52 2.00e-01 2.50e+01 6.88e+00
  chirality pdb=" C14 CLR B 401 "
            pdb=" C13 CLR B 401 "
            pdb=" C15 CLR B 401 "
            pdb=" C8  CLR B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.84    0.52 2.00e-01 2.50e+01 6.77e+00
  chirality pdb=" C10 CLR A 401 "
            pdb=" C1  CLR A 401 "
            pdb=" C5  CLR A 401 "
            pdb=" C9  CLR A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.49   -0.36 2.00e-01 2.50e+01 3.18e+00
  ... (remaining 793 not shown)

  Planarity restraints: 904
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 313 "   -0.007 2.00e-02 2.50e+03   1.45e-02 2.10e+00
        pdb=" C   PRO B 313 "    0.025 2.00e-02 2.50e+03
        pdb=" O   PRO B 313 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   PHE B 314 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 313 "    0.007 2.00e-02 2.50e+03   1.45e-02 2.10e+00
        pdb=" C   PRO A 313 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   PRO A 313 "    0.009 2.00e-02 2.50e+03
        pdb=" N   PHE A 314 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 307 "    0.007 2.00e-02 2.50e+03   1.30e-02 1.69e+00
        pdb=" C   VAL A 307 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   VAL A 307 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LEU A 308 "    0.008 2.00e-02 2.50e+03
  ... (remaining 901 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.86: 1925
        2.86 -     3.37: 5619
        3.37 -     3.88: 8442
        3.88 -     4.39: 8547
        4.39 -     4.90: 14431
  Nonbonded interactions: 38964
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 332 "
            pdb=" OG  SER B 335 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   LYS A 332 "
            pdb=" OG  SER A 335 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" OG  SER B 157 "
            pdb=" NH1 ARG B 220 "
     model   vdw
     2.436 3.120
  nonbonded pdb=" OG  SER A 157 "
            pdb=" NH1 ARG A 220 "
     model   vdw
     2.436 3.120
  nonbonded pdb=" O   VAL B 159 "
            pdb=" N   ALA B 162 "
     model   vdw
     2.443 3.120
  ... (remaining 38959 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.750
  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:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.240
  Find NCS groups from input model:        0.040
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
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      :  0.011   0.681   5471  Z= 0.953
  Angle     :  0.774   9.312   7404  Z= 0.392
  Chirality :  0.054   0.525    796
  Planarity :  0.003   0.024    904
  Dihedral  : 13.915  88.339   2074
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  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:  0.27 (0.32), residues: 618
  helix:  0.94 (0.20), residues: 530
  sheet:  None (None), residues: 0
  loop : -4.45 (0.59), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 152 
 TYR   0.016   0.002   TYR B  33 
 PHE   0.016   0.001   PHE A 219 
 TRP   0.010   0.001   TRP A 193 
 HIS   0.002   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 ( 5470)
  covalent geometry    : angle       0.77396 ( 7404)
  hydrogen bonds       : bond        0.11008 (  452)
  hydrogen bonds       : angle       5.17977 ( 1356)
  Misc. bond           : bond        0.68126 (    1)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8727 (mtt) cc_final: 0.8420 (ppp)
REVERT: A  145 ILE cc_start: 0.8404 (tt) cc_final: 0.8183 (tt)
REVERT: A  154 LEU cc_start: 0.8208 (mm) cc_final: 0.7425 (tt)
REVERT: A  228 MET cc_start: 0.8435 (ttt) cc_final: 0.7824 (ttm)
REVERT: A  239 TYR cc_start: 0.8022 (t80) cc_final: 0.7550 (m-80)
REVERT: B   87 MET cc_start: 0.8724 (mtt) cc_final: 0.8420 (ppp)
REVERT: B  145 ILE cc_start: 0.8393 (tt) cc_final: 0.8169 (tt)
REVERT: B  154 LEU cc_start: 0.8205 (mm) cc_final: 0.7428 (tt)
REVERT: B  228 MET cc_start: 0.8434 (ttt) cc_final: 0.7817 (ttm)
REVERT: B  239 TYR cc_start: 0.8015 (t80) cc_final: 0.7542 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0990
  time to fit residues: 19.3003
Evaluate side-chains
  119 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN
A 241 GLN
A 330 HIS
B 165 ASN
B 241 GLN
B 330 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.157402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.117962 restraints weight = 9097.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.122129 restraints weight = 4320.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.124739 restraints weight = 2899.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.125890 restraints weight = 2334.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.126829 restraints weight = 2103.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5471  Z= 0.155
  Angle     :  0.604   5.812   7404  Z= 0.302
  Chirality :  0.034   0.133    796
  Planarity :  0.004   0.028    904
  Dihedral  :  5.049  32.334    810
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.96 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.07 (0.34), residues: 618
  helix:  2.83 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -4.08 (0.65), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  14 
 TYR   0.011   0.001   TYR B 171 
 PHE   0.018   0.001   PHE B 235 
 TRP   0.012   0.001   TRP B 305 
 HIS   0.009   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 5470)
  covalent geometry    : angle       0.60385 ( 7404)
  hydrogen bonds       : bond        0.05638 (  452)
  hydrogen bonds       : angle       3.94616 ( 1356)
  Misc. bond           : bond        0.00370 (    1)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8687 (mtt) cc_final: 0.8447 (ppp)
REVERT: A  238 TYR cc_start: 0.7966 (t80) cc_final: 0.7627 (t80)
REVERT: A  319 LEU cc_start: 0.8964 (tt) cc_final: 0.8693 (tp)
REVERT: B   31 ARG cc_start: 0.9144 (tmm160) cc_final: 0.8860 (ttp80)
REVERT: B   87 MET cc_start: 0.8673 (mtt) cc_final: 0.8436 (ppp)
REVERT: B  238 TYR cc_start: 0.7956 (t80) cc_final: 0.7621 (t80)
REVERT: B  319 LEU cc_start: 0.8962 (tt) cc_final: 0.8695 (tp)
  outliers start: 15
  outliers final: 12
  residues processed: 130
  average time/residue: 0.0657
  time to fit residues: 11.1851
Evaluate side-chains
  118 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  244 CYS
Chi-restraints excluded: chain A residue  330 HIS
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  244 CYS
Chi-restraints excluded: chain B residue  330 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    0.3980
   chunk 2 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   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  30 HIS
** B  30 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 = 0.4297 r_free = 0.4297 target = 0.160525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.121393 restraints weight = 9096.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.125620 restraints weight = 4233.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.128339 restraints weight = 2819.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.129814 restraints weight = 2256.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.129831 restraints weight = 2006.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5471  Z= 0.142
  Angle     :  0.568   6.995   7404  Z= 0.288
  Chirality :  0.034   0.122    796
  Planarity :  0.004   0.034    904
  Dihedral  :  4.522  30.770    810
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.37 %
    Favored  : 77.29 %
  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:  3.98 (0.35), residues: 618
  helix:  3.46 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -3.88 (0.68), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  14 
 TYR   0.012   0.001   TYR A 171 
 PHE   0.015   0.001   PHE B 219 
 TRP   0.011   0.001   TRP A 305 
 HIS   0.011   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5470)
  covalent geometry    : angle       0.56806 ( 7404)
  hydrogen bonds       : bond        0.05430 (  452)
  hydrogen bonds       : angle       3.74247 ( 1356)
  Misc. bond           : bond        0.00185 (    1)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8725 (mtt) cc_final: 0.8465 (ppp)
REVERT: A  237 GLN cc_start: 0.7380 (tm-30) cc_final: 0.7098 (tm-30)
REVERT: A  238 TYR cc_start: 0.7929 (t80) cc_final: 0.7707 (t80)
REVERT: A  319 LEU cc_start: 0.8949 (tt) cc_final: 0.8675 (tp)
REVERT: B   87 MET cc_start: 0.8708 (mtt) cc_final: 0.8464 (ppp)
REVERT: B  237 GLN cc_start: 0.7391 (tm-30) cc_final: 0.7104 (tm-30)
REVERT: B  238 TYR cc_start: 0.7917 (t80) cc_final: 0.7695 (t80)
REVERT: B  319 LEU cc_start: 0.8987 (tt) cc_final: 0.8724 (tp)
  outliers start: 19
  outliers final: 15
  residues processed: 123
  average time/residue: 0.0705
  time to fit residues: 11.1526
Evaluate side-chains
  122 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ASP
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain B residue  334 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.160051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.120959 restraints weight = 9123.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.125076 restraints weight = 4323.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.127667 restraints weight = 2918.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.128722 restraints weight = 2367.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.129801 restraints weight = 2146.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5471  Z= 0.139
  Angle     :  0.556   7.707   7404  Z= 0.279
  Chirality :  0.033   0.122    796
  Planarity :  0.004   0.039    904
  Dihedral  :  4.238  27.451    810
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 21.13 %
    Favored  : 75.35 %
  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:  4.40 (0.35), residues: 618
  helix:  3.68 (0.21), residues: 530
  sheet:  None (None), residues: 0
  loop : -2.77 (0.73), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  14 
 TYR   0.011   0.001   TYR A 171 
 PHE   0.016   0.001   PHE B 219 
 TRP   0.010   0.001   TRP B 305 
 HIS   0.001   0.000   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5470)
  covalent geometry    : angle       0.55613 ( 7404)
  hydrogen bonds       : bond        0.05229 (  452)
  hydrogen bonds       : angle       3.64681 ( 1356)
  Misc. bond           : bond        0.00190 (    1)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8720 (mtt) cc_final: 0.8303 (tmm)
REVERT: A  238 TYR cc_start: 0.7836 (t80) cc_final: 0.7631 (t80)
REVERT: A  319 LEU cc_start: 0.9001 (tt) cc_final: 0.8733 (tp)
REVERT: B   87 MET cc_start: 0.8728 (mtt) cc_final: 0.8300 (tmm)
REVERT: B  238 TYR cc_start: 0.7825 (t80) cc_final: 0.7620 (t80)
REVERT: B  319 LEU cc_start: 0.9015 (tt) cc_final: 0.8743 (tp)
  outliers start: 20
  outliers final: 16
  residues processed: 120
  average time/residue: 0.0598
  time to fit residues: 9.8385
Evaluate side-chains
  121 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ASP
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  244 CYS
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  244 CYS
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain B residue  334 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0270
   chunk 31 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
B  30 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.162359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.123134 restraints weight = 9141.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.127468 restraints weight = 4314.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.130129 restraints weight = 2886.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.131658 restraints weight = 2336.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.131732 restraints weight = 2077.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5471  Z= 0.127
  Angle     :  0.559   9.240   7404  Z= 0.272
  Chirality :  0.033   0.129    796
  Planarity :  0.004   0.044    904
  Dihedral  :  3.990  25.117    810
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 23.42 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  4.60 (0.34), residues: 618
  helix:  3.80 (0.21), residues: 530
  sheet:  None (None), residues: 0
  loop : -2.49 (0.77), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  14 
 TYR   0.011   0.001   TYR B 171 
 PHE   0.021   0.001   PHE B 235 
 TRP   0.009   0.001   TRP B 305 
 HIS   0.002   0.000   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5470)
  covalent geometry    : angle       0.55930 ( 7404)
  hydrogen bonds       : bond        0.04848 (  452)
  hydrogen bonds       : angle       3.53814 ( 1356)
  Misc. bond           : bond        0.00170 (    1)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.9529 (tt) cc_final: 0.9275 (pp)
REVERT: A   87 MET cc_start: 0.8765 (mtt) cc_final: 0.8318 (tmm)
REVERT: A  319 LEU cc_start: 0.9004 (tt) cc_final: 0.8751 (tp)
REVERT: B   87 MET cc_start: 0.8773 (mtt) cc_final: 0.8306 (tmm)
REVERT: B  319 LEU cc_start: 0.8977 (tt) cc_final: 0.8723 (tp)
  outliers start: 14
  outliers final: 12
  residues processed: 118
  average time/residue: 0.0554
  time to fit residues: 9.0294
Evaluate side-chains
  111 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ASP
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain B residue  334 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0980
   chunk 8 optimal weight:    5.9990
   chunk 47 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.9184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.160878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.121563 restraints weight = 9154.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.125754 restraints weight = 4328.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.128286 restraints weight = 2924.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.129537 restraints weight = 2373.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.130482 restraints weight = 2142.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5471  Z= 0.139
  Angle     :  0.588   8.358   7404  Z= 0.286
  Chirality :  0.034   0.141    796
  Planarity :  0.003   0.027    904
  Dihedral  :  3.919  20.275    810
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 24.82 %
    Favored  : 71.48 %
  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:  4.66 (0.35), residues: 618
  helix:  3.82 (0.21), residues: 530
  sheet:  None (None), residues: 0
  loop : -2.40 (0.78), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  14 
 TYR   0.022   0.001   TYR B 238 
 PHE   0.016   0.001   PHE A 219 
 TRP   0.009   0.001   TRP B 305 
 HIS   0.003   0.000   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 5470)
  covalent geometry    : angle       0.58787 ( 7404)
  hydrogen bonds       : bond        0.04990 (  452)
  hydrogen bonds       : angle       3.59312 ( 1356)
  Misc. bond           : bond        0.00189 (    1)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8733 (mtt) cc_final: 0.8305 (tmm)
REVERT: A  319 LEU cc_start: 0.9052 (tt) cc_final: 0.8775 (tp)
REVERT: B   87 MET cc_start: 0.8740 (mtt) cc_final: 0.8296 (tmm)
REVERT: B  319 LEU cc_start: 0.9032 (tt) cc_final: 0.8751 (tp)
  outliers start: 21
  outliers final: 13
  residues processed: 116
  average time/residue: 0.0532
  time to fit residues: 8.5372
Evaluate side-chains
  114 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ASP
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  244 CYS
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain B residue  334 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.1786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.164481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.123896 restraints weight = 8818.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.127924 restraints weight = 4301.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.130441 restraints weight = 2867.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.131961 restraints weight = 2293.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.132705 restraints weight = 2023.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5471  Z= 0.154
  Angle     :  0.645  11.883   7404  Z= 0.304
  Chirality :  0.038   0.288    796
  Planarity :  0.004   0.028    904
  Dihedral  :  3.962  17.534    810
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 23.94 %
    Favored  : 72.36 %
  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:  4.55 (0.35), residues: 618
  helix:  3.74 (0.21), residues: 530
  sheet:  None (None), residues: 0
  loop : -2.36 (0.78), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  14 
 TYR   0.023   0.002   TYR A 238 
 PHE   0.016   0.001   PHE B 219 
 TRP   0.010   0.001   TRP B 305 
 HIS   0.002   0.000   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5470)
  covalent geometry    : angle       0.64536 ( 7404)
  hydrogen bonds       : bond        0.05212 (  452)
  hydrogen bonds       : angle       3.67451 ( 1356)
  Misc. bond           : bond        0.00204 (    1)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8717 (mtt) cc_final: 0.8306 (tmm)
REVERT: A  237 GLN cc_start: 0.7273 (tm-30) cc_final: 0.7012 (tm-30)
REVERT: A  319 LEU cc_start: 0.9059 (tt) cc_final: 0.8793 (tp)
REVERT: B   87 MET cc_start: 0.8732 (mtt) cc_final: 0.8294 (tmm)
REVERT: B  237 GLN cc_start: 0.7324 (tm-30) cc_final: 0.7057 (tm-30)
REVERT: B  319 LEU cc_start: 0.9041 (tt) cc_final: 0.8769 (tp)
  outliers start: 21
  outliers final: 18
  residues processed: 115
  average time/residue: 0.0570
  time to fit residues: 8.9112
Evaluate side-chains
  121 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ASP
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  244 CYS
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain B residue  334 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0060
   chunk 9 optimal weight:    0.4980
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.5396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.161503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.122431 restraints weight = 8987.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.126529 restraints weight = 4452.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.129017 restraints weight = 3066.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.130098 restraints weight = 2502.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.130099 restraints weight = 2271.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.4353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5471  Z= 0.124
  Angle     :  0.613  10.755   7404  Z= 0.286
  Chirality :  0.035   0.247    796
  Planarity :  0.004   0.048    904
  Dihedral  :  3.852  21.940    810
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 25.18 %
    Favored  : 73.06 %
  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:  4.56 (0.34), residues: 618
  helix:  3.75 (0.21), residues: 530
  sheet:  None (None), residues: 0
  loop : -2.34 (0.76), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  31 
 TYR   0.019   0.001   TYR A 238 
 PHE   0.023   0.001   PHE B 235 
 TRP   0.011   0.001   TRP A 305 
 HIS   0.002   0.000   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5470)
  covalent geometry    : angle       0.61258 ( 7404)
  hydrogen bonds       : bond        0.04605 (  452)
  hydrogen bonds       : angle       3.50275 ( 1356)
  Misc. bond           : bond        0.00156 (    1)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8764 (mtt) cc_final: 0.8304 (tmm)
REVERT: A  237 GLN cc_start: 0.7316 (tm-30) cc_final: 0.7027 (tm-30)
REVERT: A  319 LEU cc_start: 0.9040 (tt) cc_final: 0.8782 (tp)
REVERT: B   87 MET cc_start: 0.8772 (mtt) cc_final: 0.8295 (tmm)
REVERT: B  237 GLN cc_start: 0.7334 (tm-30) cc_final: 0.7015 (tm-30)
REVERT: B  319 LEU cc_start: 0.9032 (tt) cc_final: 0.8769 (tp)
REVERT: B  334 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7302 (t-170)
  outliers start: 10
  outliers final: 8
  residues processed: 110
  average time/residue: 0.0441
  time to fit residues: 7.1292
Evaluate side-chains
  111 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ASP
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue  244 CYS
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain B residue  334 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 31 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    0.2980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.163100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.124421 restraints weight = 9129.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.128653 restraints weight = 4436.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.131199 restraints weight = 2995.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.132366 restraints weight = 2429.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.133151 restraints weight = 2192.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5471  Z= 0.126
  Angle     :  0.616  10.647   7404  Z= 0.288
  Chirality :  0.035   0.215    796
  Planarity :  0.004   0.035    904
  Dihedral  :  3.831  20.207    810
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 24.30 %
    Favored  : 73.24 %
  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:  4.59 (0.34), residues: 618
  helix:  3.72 (0.21), residues: 534
  sheet:  None (None), residues: 0
  loop : -2.28 (0.80), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  31 
 TYR   0.017   0.001   TYR A 238 
 PHE   0.023   0.001   PHE B 235 
 TRP   0.008   0.001   TRP B 305 
 HIS   0.002   0.000   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 5470)
  covalent geometry    : angle       0.61586 ( 7404)
  hydrogen bonds       : bond        0.04617 (  452)
  hydrogen bonds       : angle       3.50590 ( 1356)
  Misc. bond           : bond        0.00160 (    1)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8720 (mtt) cc_final: 0.8278 (tmm)
REVERT: A  319 LEU cc_start: 0.9041 (tt) cc_final: 0.8786 (tp)
REVERT: A  334 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7289 (t-170)
REVERT: B   87 MET cc_start: 0.8733 (mtt) cc_final: 0.8270 (tmm)
REVERT: B  319 LEU cc_start: 0.9046 (tt) cc_final: 0.8784 (tp)
REVERT: B  334 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7276 (t-170)
  outliers start: 14
  outliers final: 11
  residues processed: 110
  average time/residue: 0.0527
  time to fit residues: 8.3086
Evaluate side-chains
  112 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ASP
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  244 CYS
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain B residue  334 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 44 optimal weight:    0.4980
   chunk 23 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.160949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.121909 restraints weight = 9122.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.126044 restraints weight = 4467.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.128552 restraints weight = 3043.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.129775 restraints weight = 2474.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.130589 restraints weight = 2229.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.4608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5471  Z= 0.134
  Angle     :  0.636  10.269   7404  Z= 0.299
  Chirality :  0.036   0.211    796
  Planarity :  0.004   0.034    904
  Dihedral  :  3.821  19.498    810
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 25.35 %
    Favored  : 72.36 %
  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:  4.57 (0.35), residues: 618
  helix:  3.70 (0.21), residues: 534
  sheet:  None (None), residues: 0
  loop : -2.29 (0.80), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  31 
 TYR   0.017   0.001   TYR B 238 
 PHE   0.023   0.001   PHE B 235 
 TRP   0.009   0.001   TRP B 193 
 HIS   0.002   0.000   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 5470)
  covalent geometry    : angle       0.63613 ( 7404)
  hydrogen bonds       : bond        0.04662 (  452)
  hydrogen bonds       : angle       3.50291 ( 1356)
  Misc. bond           : bond        0.00170 (    1)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLN cc_start: 0.8694 (tt0) cc_final: 0.7996 (tp-100)
REVERT: A   32 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9225 (tp)
REVERT: A   87 MET cc_start: 0.8704 (mtt) cc_final: 0.8263 (tmm)
REVERT: A  237 GLN cc_start: 0.7319 (tm-30) cc_final: 0.6875 (tm-30)
REVERT: A  319 LEU cc_start: 0.9047 (tt) cc_final: 0.8791 (tp)
REVERT: A  334 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7255 (t-170)
REVERT: B   87 MET cc_start: 0.8724 (mtt) cc_final: 0.8259 (tmm)
REVERT: B  237 GLN cc_start: 0.7340 (tm-30) cc_final: 0.6900 (tm-30)
REVERT: B  319 LEU cc_start: 0.9042 (tt) cc_final: 0.8784 (tp)
REVERT: B  334 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7226 (t-170)
  outliers start: 13
  outliers final: 9
  residues processed: 109
  average time/residue: 0.0378
  time to fit residues: 6.2784
Evaluate side-chains
  111 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ASP
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue  244 CYS
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain B residue  334 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0570
   chunk 60 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.5498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.163200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.123968 restraints weight = 9038.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.128126 restraints weight = 4599.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.130586 restraints weight = 3189.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.131650 restraints weight = 2626.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.132600 restraints weight = 2390.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.4828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5471  Z= 0.124
  Angle     :  0.609  10.172   7404  Z= 0.283
  Chirality :  0.035   0.202    796
  Planarity :  0.003   0.032    904
  Dihedral  :  3.712  21.359    810
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 26.58 %
    Favored  : 72.01 %
  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:  4.66 (0.35), residues: 618
  helix:  3.76 (0.21), residues: 534
  sheet:  None (None), residues: 0
  loop : -2.23 (0.81), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  31 
 TYR   0.014   0.001   TYR B 238 
 PHE   0.024   0.001   PHE B 235 
 TRP   0.008   0.001   TRP B 193 
 HIS   0.002   0.000   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 5470)
  covalent geometry    : angle       0.60856 ( 7404)
  hydrogen bonds       : bond        0.04381 (  452)
  hydrogen bonds       : angle       3.39400 ( 1356)
  Misc. bond           : bond        0.00153 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 919.19 seconds
wall clock time: 16 minutes 28.62 seconds (988.62 seconds total)