Starting phenix.real_space_refine
on Tue Mar  3 12:29:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8de7_27386/03_2026/8de7_27386.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8de7_27386/03_2026/8de7_27386.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8de7_27386/03_2026/8de7_27386.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8de7_27386/03_2026/8de7_27386.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8de7_27386/03_2026/8de7_27386.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8de7_27386/03_2026/8de7_27386.cif"
  }
  resolution = 3.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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
     K       3      8.98       5
     S      16      5.16       5
     C    2789      2.51       5
     N     637      2.21       5
     O     723      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 4168
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2067
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 2067
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 7, 'TRANS': 255}
    Chain: "A"
      Number of atoms: 2063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 2063
          Classifications: {'peptide': 263}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 255}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {'  K': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 0.96, per 1000 atoms: 0.23
  Number of scatterers: 4168
  At special positions: 0
  Unit cell: (80.7, 79.624, 94.688, 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)
     K       3     19.00
     S      16     16.00
     O     723      8.00
     N     637      7.00
     C    2789      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  93 " - pdb=" SG  CYS A  93 " 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: 0.33
  Conformation dependent library (CDL) restraints added in 117.5 milliseconds
  

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  956

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      79.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'B' and resid 43 through 91
      Proline residue:  B  71  - end of helix
    Processing helix  chain 'B' and resid 95 through 113
    Processing helix  chain 'B' and resid 128 through 142
    Processing helix  chain 'B' and resid 152 through 194
      removed outlier: 3.738A  pdb=" N   ILE B 157 " --> pdb=" O   GLU B 153 " (cutoff:3.500A)
      Proline residue:  B 168  - end of helix
      removed outlier: 4.078A  pdb=" N   LYS B 194 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 223
    Processing helix  chain 'B' and resid 224 through 235
    Processing helix  chain 'B' and resid 237 through 251
      removed outlier: 3.641A  pdb=" N   ILE B 242 " --> pdb=" O   ALA B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 302
    Processing helix  chain 'A' and resid 43 through 91
      Proline residue:  A  71  - end of helix
    Processing helix  chain 'A' and resid 95 through 113
    Processing helix  chain 'A' and resid 128 through 142
    Processing helix  chain 'A' and resid 152 through 197
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 202 through 223
      removed outlier: 3.888A  pdb=" N   ARG A 207 " --> pdb=" O   GLN A 203 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU A 221 " --> pdb=" O   PHE A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 234
    Processing helix  chain 'A' and resid 237 through 250
    Processing helix  chain 'A' and resid 270 through 301
      removed outlier: 3.982A  pdb=" N   ALA A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   TYR A 284 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LYS A 301 " --> pdb=" O   ARG A 297 " (cutoff:3.500A)

    334 hydrogen bonds defined for protein.
    1002 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: 0.53

  Time building geometry restraints manager: 0.44 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: 1199
        1.34 -     1.46: 807
        1.46 -     1.58: 2240
        1.58 -     1.69: 0
        1.69 -     1.81: 26
  Bond restraints: 4272
  Sorted by residual:
  bond pdb=" C1B LMT B 401 "
       pdb=" O5B LMT B 401 "
    ideal  model  delta    sigma   weight residual
    1.393  1.502 -0.109 2.00e-02 2.50e+03 2.96e+01
  bond pdb=" C1' LMT B 401 "
       pdb=" O5' LMT B 401 "
    ideal  model  delta    sigma   weight residual
    1.408  1.503 -0.095 2.00e-02 2.50e+03 2.25e+01
  bond pdb=" C5' LMT B 401 "
       pdb=" O5' LMT B 401 "
    ideal  model  delta    sigma   weight residual
    1.411  1.473 -0.062 2.00e-02 2.50e+03 9.76e+00
  bond pdb=" C5B LMT B 401 "
       pdb=" O5B LMT B 401 "
    ideal  model  delta    sigma   weight residual
    1.422  1.479 -0.057 2.00e-02 2.50e+03 8.18e+00
  bond pdb=" C3B LMT B 401 "
       pdb=" O3B LMT B 401 "
    ideal  model  delta    sigma   weight residual
    1.406  1.458 -0.052 2.00e-02 2.50e+03 6.89e+00
  ... (remaining 4267 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 5578
        2.51 -     5.02: 186
        5.02 -     7.52: 34
        7.52 -    10.03: 3
       10.03 -    12.54: 2
  Bond angle restraints: 5803
  Sorted by residual:
  angle pdb=" N   VAL A 197 "
        pdb=" CA  VAL A 197 "
        pdb=" C   VAL A 197 "
      ideal   model   delta    sigma   weight residual
     110.62  114.52   -3.90 1.02e+00 9.61e-01 1.46e+01
  angle pdb=" N   GLY A 166 "
        pdb=" CA  GLY A 166 "
        pdb=" C   GLY A 166 "
      ideal   model   delta    sigma   weight residual
     112.77  117.60   -4.83 1.28e+00 6.10e-01 1.42e+01
  angle pdb=" CA  LEU A 267 "
        pdb=" CB  LEU A 267 "
        pdb=" CG  LEU A 267 "
      ideal   model   delta    sigma   weight residual
     116.30  128.84  -12.54 3.50e+00 8.16e-02 1.28e+01
  angle pdb=" CA  LEU B 169 "
        pdb=" CB  LEU B 169 "
        pdb=" CG  LEU B 169 "
      ideal   model   delta    sigma   weight residual
     116.30  128.68  -12.38 3.50e+00 8.16e-02 1.25e+01
  angle pdb=" CA  THR B 152 "
        pdb=" CB  THR B 152 "
        pdb=" CG2 THR B 152 "
      ideal   model   delta    sigma   weight residual
     110.50  116.33   -5.83 1.70e+00 3.46e-01 1.18e+01
  ... (remaining 5798 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.63: 2230
       19.63 -    39.27: 194
       39.27 -    58.90: 36
       58.90 -    78.53: 5
       78.53 -    98.16: 13
  Dihedral angle restraints: 2478
    sinusoidal: 982
      harmonic: 1496
  Sorted by residual:
  dihedral pdb=" CB  CYS B  93 "
           pdb=" SG  CYS B  93 "
           pdb=" SG  CYS A  93 "
           pdb=" CB  CYS A  93 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.74   79.74     1      1.00e+01 1.00e-02 7.89e+01
  dihedral pdb=" O2B LMT B 401 "
           pdb=" C1B LMT B 401 "
           pdb=" C2B LMT B 401 "
           pdb=" O5B LMT B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -176.42  -78.26  -98.16     1      3.00e+01 1.11e-03 1.22e+01
  dihedral pdb=" C3B LMT B 401 "
           pdb=" C1B LMT B 401 "
           pdb=" C2B LMT B 401 "
           pdb=" O5B LMT B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -53.08   43.42  -96.50     1      3.00e+01 1.11e-03 1.19e+01
  ... (remaining 2475 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 499
       0.052 -    0.103: 125
       0.103 -    0.155: 49
       0.155 -    0.206: 7
       0.206 -    0.258: 8
  Chirality restraints: 688
  Sorted by residual:
  chirality pdb=" CB  THR A 138 "
            pdb=" CA  THR A 138 "
            pdb=" OG1 THR A 138 "
            pdb=" CG2 THR A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.29    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  GLN B  70 "
            pdb=" N   GLN B  70 "
            pdb=" C   GLN B  70 "
            pdb=" CB  GLN B  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CG  LEU B 169 "
            pdb=" CB  LEU B 169 "
            pdb=" CD1 LEU B 169 "
            pdb=" CD2 LEU B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.84    0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 685 not shown)

  Planarity restraints: 692
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 149 "   -0.046 5.00e-02 4.00e+02   6.94e-02 7.70e+00
        pdb=" N   PRO B 150 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B 150 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 150 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 115 "    0.046 5.00e-02 4.00e+02   6.86e-02 7.53e+00
        pdb=" N   PRO A 116 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 116 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 116 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 149 "    0.044 5.00e-02 4.00e+02   6.68e-02 7.13e+00
        pdb=" N   PRO A 150 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "    0.037 5.00e-02 4.00e+02
  ... (remaining 689 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.87: 1466
        2.87 -     3.44: 5212
        3.44 -     4.01: 7477
        4.01 -     4.57: 10627
        4.57 -     5.14: 14643
  Nonbonded interactions: 39425
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 121 "
            pdb=" OG  SER B 124 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OE2 GLU A 234 "
            pdb=" OH  TYR A 266 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" NZ  LYS B  84 "
            pdb=" O   PRO A 116 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" O   ALA A 287 "
            pdb=" OG  SER A 290 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" O   ARG A 111 "
            pdb=" NE2 HIS A 151 "
     model   vdw
     2.380 3.120
  ... (remaining 39420 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 41 through 301)
  selection = (chain 'B' and resid 41 through 301)
}

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 individual isotropic
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:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.430
  Find NCS groups from input model:        0.070
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
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      :  0.006   0.109   4273  Z= 0.302
  Angle     :  1.055  12.541   5805  Z= 0.578
  Chirality :  0.058   0.258    688
  Planarity :  0.008   0.069    692
  Dihedral  : 16.507  98.164   1519
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  0.22 %
    Favored  : 98.88 %
  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:  4.08 (0.33), residues: 522
  helix:  3.44 (0.22), residues: 402
  sheet:  None (None), residues: 0
  loop : -0.10 (0.51), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 207 
 TYR   0.017   0.003   TYR B 266 
 PHE   0.023   0.003   PHE A 285 
 TRP   0.033   0.003   TRP A 199 
 HIS   0.006   0.002   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00636 ( 4272)
  covalent geometry    : angle       1.05109 ( 5803)
  SS BOND              : bond        0.00150 (    1)
  SS BOND              : angle       5.25403 (    2)
  hydrogen bonds       : bond        0.08583 (  334)
  hydrogen bonds       : angle       4.65791 ( 1002)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 251
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 LEU cc_start: 0.9398 (tp) cc_final: 0.9120 (tp)
REVERT: B   82 GLN cc_start: 0.9328 (mm110) cc_final: 0.9022 (mm-40)
REVERT: B   96 THR cc_start: 0.9353 (t) cc_final: 0.8967 (p)
REVERT: B   99 LEU cc_start: 0.9722 (tp) cc_final: 0.9386 (tp)
REVERT: B  101 ASP cc_start: 0.9448 (t0) cc_final: 0.9203 (m-30)
REVERT: B  104 LYS cc_start: 0.9481 (ttmm) cc_final: 0.9228 (mtmm)
REVERT: B  215 ILE cc_start: 0.9649 (mt) cc_final: 0.9306 (mt)
REVERT: B  231 GLN cc_start: 0.8610 (tt0) cc_final: 0.8370 (tt0)
REVERT: A   48 LEU cc_start: 0.9520 (tp) cc_final: 0.9291 (tp)
REVERT: A   52 LEU cc_start: 0.9366 (mt) cc_final: 0.9164 (mt)
REVERT: A   56 LEU cc_start: 0.9303 (tp) cc_final: 0.9048 (tp)
REVERT: A   66 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8385 (ttmm)
REVERT: A   77 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8857 (mmmm)
REVERT: A   82 GLN cc_start: 0.9406 (tp40) cc_final: 0.9141 (mm-40)
REVERT: A   95 GLN cc_start: 0.9193 (mm110) cc_final: 0.8634 (mm110)
REVERT: A  101 ASP cc_start: 0.9146 (m-30) cc_final: 0.7925 (m-30)
REVERT: A  104 LYS cc_start: 0.9540 (ttpp) cc_final: 0.9311 (mtmm)
REVERT: A  105 GLN cc_start: 0.9524 (mm110) cc_final: 0.9259 (mm-40)
REVERT: A  191 LYS cc_start: 0.8595 (mttp) cc_final: 0.8100 (ttmm)
REVERT: A  196 PHE cc_start: 0.9018 (t80) cc_final: 0.8692 (t80)
REVERT: A  216 LEU cc_start: 0.9372 (mp) cc_final: 0.9109 (mp)
REVERT: A  225 LEU cc_start: 0.9268 (tp) cc_final: 0.9038 (tp)
REVERT: A  269 TYR cc_start: 0.8095 (m-80) cc_final: 0.7592 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 253
  average time/residue: 0.0642
  time to fit residues: 20.4302
Evaluate side-chains
  213 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  76 GLN
** A  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 GLN
A 200 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.153408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.105997 restraints weight = 7194.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 4.00
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4273  Z= 0.184
  Angle     :  0.775  12.769   5805  Z= 0.383
  Chirality :  0.046   0.286    688
  Planarity :  0.005   0.047    692
  Dihedral  :  9.240  59.214    612
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 20.00 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.72 (0.35), residues: 522
  helix:  3.20 (0.23), residues: 408
  sheet:  None (None), residues: 0
  loop : -0.50 (0.55), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  79 
 TYR   0.015   0.002   TYR B 162 
 PHE   0.019   0.002   PHE A 244 
 TRP   0.015   0.002   TRP A 277 
 HIS   0.004   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 4272)
  covalent geometry    : angle       0.77439 ( 5803)
  SS BOND              : bond        0.00321 (    1)
  SS BOND              : angle       1.87761 (    2)
  hydrogen bonds       : bond        0.04623 (  334)
  hydrogen bonds       : angle       4.19857 ( 1002)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 218
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 GLN cc_start: 0.9502 (mm110) cc_final: 0.9198 (mm-40)
REVERT: B   98 GLU cc_start: 0.9508 (mp0) cc_final: 0.9281 (mp0)
REVERT: B  101 ASP cc_start: 0.9624 (t0) cc_final: 0.9265 (m-30)
REVERT: B  104 LYS cc_start: 0.9440 (ttmm) cc_final: 0.9170 (mtmm)
REVERT: B  231 GLN cc_start: 0.9116 (tt0) cc_final: 0.8482 (tt0)
REVERT: B  269 TYR cc_start: 0.8201 (m-80) cc_final: 0.7939 (m-80)
REVERT: A   42 MET cc_start: 0.8441 (mmm) cc_final: 0.8209 (mmm)
REVERT: A   48 LEU cc_start: 0.9478 (tp) cc_final: 0.9237 (tp)
REVERT: A   52 LEU cc_start: 0.9529 (mt) cc_final: 0.9306 (mt)
REVERT: A   56 LEU cc_start: 0.9621 (tp) cc_final: 0.9400 (tp)
REVERT: A  101 ASP cc_start: 0.8693 (m-30) cc_final: 0.8411 (m-30)
REVERT: A  104 LYS cc_start: 0.9591 (ttpp) cc_final: 0.9255 (mtmm)
REVERT: A  216 LEU cc_start: 0.9467 (mp) cc_final: 0.9243 (mp)
REVERT: A  269 TYR cc_start: 0.8414 (m-80) cc_final: 0.7952 (m-80)
  outliers start: 17
  outliers final: 8
  residues processed: 221
  average time/residue: 0.0568
  time to fit residues: 16.1953
Evaluate side-chains
  210 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 202
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain A residue   93 CYS
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  278 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   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  91 HIS
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 232 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.151352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.100023 restraints weight = 7301.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 4.29
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   4273  Z= 0.182
  Angle     :  0.744  10.036   5805  Z= 0.375
  Chirality :  0.045   0.289    688
  Planarity :  0.005   0.058    692
  Dihedral  :  7.418  46.843    611
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.92 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.29 (0.35), residues: 522
  helix:  2.96 (0.23), residues: 407
  sheet:  None (None), residues: 0
  loop : -0.93 (0.54), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  79 
 TYR   0.019   0.002   TYR A 266 
 PHE   0.020   0.001   PHE A 158 
 TRP   0.015   0.001   TRP A 277 
 HIS   0.006   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 4272)
  covalent geometry    : angle       0.74319 ( 5803)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       1.62674 (    2)
  hydrogen bonds       : bond        0.04212 (  334)
  hydrogen bonds       : angle       4.11476 ( 1002)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 209
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 GLN cc_start: 0.9507 (mm110) cc_final: 0.9140 (mm-40)
REVERT: B  101 ASP cc_start: 0.9654 (t0) cc_final: 0.9316 (m-30)
REVERT: B  104 LYS cc_start: 0.9424 (ttmm) cc_final: 0.9166 (mtmm)
REVERT: B  231 GLN cc_start: 0.8998 (tt0) cc_final: 0.8275 (tt0)
REVERT: B  269 TYR cc_start: 0.8168 (m-80) cc_final: 0.7939 (m-80)
REVERT: A   42 MET cc_start: 0.8510 (mmm) cc_final: 0.8198 (mmm)
REVERT: A   48 LEU cc_start: 0.9478 (tp) cc_final: 0.9243 (tp)
REVERT: A   51 PHE cc_start: 0.9194 (t80) cc_final: 0.8969 (t80)
REVERT: A   52 LEU cc_start: 0.9555 (mt) cc_final: 0.9349 (mt)
REVERT: A   56 LEU cc_start: 0.9619 (tp) cc_final: 0.9402 (tp)
REVERT: A   98 GLU cc_start: 0.9031 (pt0) cc_final: 0.8799 (pt0)
REVERT: A   99 LEU cc_start: 0.9431 (pp) cc_final: 0.8896 (pp)
REVERT: A  104 LYS cc_start: 0.9568 (ttpp) cc_final: 0.9265 (mtmm)
REVERT: A  122 GLN cc_start: 0.8705 (pm20) cc_final: 0.8391 (pm20)
REVERT: A  228 LEU cc_start: 0.9554 (mm) cc_final: 0.9345 (mm)
REVERT: A  240 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8372 (mt-10)
REVERT: A  269 TYR cc_start: 0.8432 (m-80) cc_final: 0.7988 (m-80)
  outliers start: 14
  outliers final: 9
  residues processed: 213
  average time/residue: 0.0511
  time to fit residues: 14.0944
Evaluate side-chains
  212 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 203
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   93 CYS
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  219 CYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0870
   chunk 19 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 46 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 26 optimal weight:    7.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 180 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.150693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.100388 restraints weight = 7250.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 4.26
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.4240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4273  Z= 0.167
  Angle     :  0.752   9.641   5805  Z= 0.369
  Chirality :  0.044   0.253    688
  Planarity :  0.005   0.065    692
  Dihedral  :  6.232  41.138    611
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 25.17 %
    Favored  : 70.56 %
  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:  2.99 (0.36), residues: 522
  helix:  2.78 (0.24), residues: 410
  sheet:  None (None), residues: 0
  loop : -1.25 (0.57), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  79 
 TYR   0.011   0.002   TYR A 266 
 PHE   0.036   0.002   PHE A 196 
 TRP   0.009   0.001   TRP B  44 
 HIS   0.003   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 4272)
  covalent geometry    : angle       0.75162 ( 5803)
  SS BOND              : bond        0.00043 (    1)
  SS BOND              : angle       1.39327 (    2)
  hydrogen bonds       : bond        0.04055 (  334)
  hydrogen bonds       : angle       4.14261 ( 1002)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 208
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   48 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9180 (mp)
REVERT: B   82 GLN cc_start: 0.9514 (mm110) cc_final: 0.9115 (mm-40)
REVERT: B   95 GLN cc_start: 0.9177 (mp10) cc_final: 0.8883 (mp10)
REVERT: B  101 ASP cc_start: 0.9641 (t0) cc_final: 0.9307 (m-30)
REVERT: B  104 LYS cc_start: 0.9455 (ttmm) cc_final: 0.9208 (mtmm)
REVERT: B  195 MET cc_start: 0.4455 (ttp) cc_final: 0.3982 (tpp)
REVERT: B  231 GLN cc_start: 0.8989 (tt0) cc_final: 0.8272 (tt0)
REVERT: B  270 TYR cc_start: 0.8387 (t80) cc_final: 0.8035 (t80)
REVERT: B  289 LEU cc_start: 0.8712 (mp) cc_final: 0.8477 (mp)
REVERT: A   42 MET cc_start: 0.8455 (mmm) cc_final: 0.8184 (mmm)
REVERT: A   48 LEU cc_start: 0.9480 (tp) cc_final: 0.9239 (tp)
REVERT: A   51 PHE cc_start: 0.9174 (t80) cc_final: 0.8949 (t80)
REVERT: A   52 LEU cc_start: 0.9556 (mt) cc_final: 0.9348 (mt)
REVERT: A   56 LEU cc_start: 0.9624 (tp) cc_final: 0.9422 (tp)
REVERT: A   98 GLU cc_start: 0.9076 (pt0) cc_final: 0.8824 (pt0)
REVERT: A   99 LEU cc_start: 0.9474 (pp) cc_final: 0.8960 (pp)
REVERT: A  100 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9024 (mm-30)
REVERT: A  104 LYS cc_start: 0.9546 (ttpp) cc_final: 0.9272 (mtmm)
REVERT: A  122 GLN cc_start: 0.8788 (pm20) cc_final: 0.8420 (pm20)
REVERT: A  240 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8388 (mt-10)
REVERT: A  263 GLU cc_start: 0.8518 (pp20) cc_final: 0.8291 (pp20)
REVERT: A  268 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7532 (p0)
REVERT: A  269 TYR cc_start: 0.8476 (m-80) cc_final: 0.7905 (m-80)
  outliers start: 19
  outliers final: 13
  residues processed: 211
  average time/residue: 0.0521
  time to fit residues: 14.2550
Evaluate side-chains
  216 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 201
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   93 CYS
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  219 CYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0010
   chunk 35 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0980
   chunk 13 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 42 optimal weight:    8.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 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 = 0.3989 r_free = 0.3989 target = 0.152951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.107923 restraints weight = 7188.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 4.02
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.4431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4273  Z= 0.155
  Angle     :  0.747   8.372   5805  Z= 0.365
  Chirality :  0.043   0.231    688
  Planarity :  0.005   0.060    692
  Dihedral  :  5.767  43.117    611
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 28.99 %
    Favored  : 67.19 %
  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:  2.77 (0.36), residues: 522
  helix:  2.61 (0.24), residues: 410
  sheet:  None (None), residues: 0
  loop : -1.27 (0.57), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 297 
 TYR   0.019   0.002   TYR B  57 
 PHE   0.017   0.001   PHE B 158 
 TRP   0.013   0.001   TRP B  44 
 HIS   0.003   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4272)
  covalent geometry    : angle       0.74626 ( 5803)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       1.32170 (    2)
  hydrogen bonds       : bond        0.03986 (  334)
  hydrogen bonds       : angle       4.16820 ( 1002)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 210
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 GLN cc_start: 0.9489 (mm110) cc_final: 0.9118 (mm-40)
REVERT: B   95 GLN cc_start: 0.9119 (mp10) cc_final: 0.8791 (mp10)
REVERT: B  101 ASP cc_start: 0.9627 (t0) cc_final: 0.9257 (m-30)
REVERT: B  104 LYS cc_start: 0.9457 (ttmm) cc_final: 0.9165 (mtmm)
REVERT: B  195 MET cc_start: 0.4100 (ttp) cc_final: 0.3756 (tpp)
REVERT: B  231 GLN cc_start: 0.8947 (tt0) cc_final: 0.8202 (tt0)
REVERT: B  240 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7895 (pt0)
REVERT: B  270 TYR cc_start: 0.8351 (t80) cc_final: 0.8077 (t80)
REVERT: B  289 LEU cc_start: 0.8768 (mp) cc_final: 0.8557 (mp)
REVERT: A   42 MET cc_start: 0.8510 (mmm) cc_final: 0.8290 (mmm)
REVERT: A   48 LEU cc_start: 0.9482 (tp) cc_final: 0.9233 (tp)
REVERT: A   51 PHE cc_start: 0.9146 (t80) cc_final: 0.8916 (t80)
REVERT: A   52 LEU cc_start: 0.9548 (mt) cc_final: 0.9326 (mt)
REVERT: A   82 GLN cc_start: 0.9540 (tp40) cc_final: 0.9209 (mm-40)
REVERT: A  104 LYS cc_start: 0.9524 (ttpp) cc_final: 0.9271 (mtmm)
REVERT: A  122 GLN cc_start: 0.8844 (pm20) cc_final: 0.8422 (pm20)
REVERT: A  151 HIS cc_start: 0.8503 (m90) cc_final: 0.7957 (m-70)
REVERT: A  172 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8302 (t80)
REVERT: A  240 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8329 (mt-10)
REVERT: A  263 GLU cc_start: 0.8581 (pp20) cc_final: 0.8347 (pp20)
REVERT: A  268 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7533 (p0)
REVERT: A  269 TYR cc_start: 0.8424 (m-80) cc_final: 0.7798 (m-80)
  outliers start: 17
  outliers final: 10
  residues processed: 214
  average time/residue: 0.0516
  time to fit residues: 14.5133
Evaluate side-chains
  211 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 199
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  219 CYS
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 41 optimal weight:   10.0000
   chunk 47 optimal weight:    0.4980
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 180 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.150935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.100400 restraints weight = 7418.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 4.28
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.4722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   4273  Z= 0.197
  Angle     :  0.794  13.906   5805  Z= 0.389
  Chirality :  0.044   0.202    688
  Planarity :  0.005   0.068    692
  Dihedral  :  5.958  46.714    611
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 32.13 %
    Favored  : 63.15 %
  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:  2.58 (0.36), residues: 522
  helix:  2.45 (0.24), residues: 410
  sheet:  None (None), residues: 0
  loop : -1.25 (0.58), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  79 
 TYR   0.014   0.002   TYR A 270 
 PHE   0.019   0.001   PHE A 158 
 TRP   0.018   0.001   TRP A 277 
 HIS   0.002   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 4272)
  covalent geometry    : angle       0.79419 ( 5803)
  SS BOND              : bond        0.00858 (    1)
  SS BOND              : angle       0.39791 (    2)
  hydrogen bonds       : bond        0.04081 (  334)
  hydrogen bonds       : angle       4.31150 ( 1002)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   95 GLN cc_start: 0.9216 (mp10) cc_final: 0.8961 (mp10)
REVERT: B  101 ASP cc_start: 0.9658 (t0) cc_final: 0.9234 (m-30)
REVERT: B  104 LYS cc_start: 0.9447 (ttmm) cc_final: 0.9143 (mtmm)
REVERT: B  195 MET cc_start: 0.4288 (ttp) cc_final: 0.3867 (tpp)
REVERT: B  231 GLN cc_start: 0.8925 (tt0) cc_final: 0.8193 (tt0)
REVERT: B  240 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7896 (pt0)
REVERT: B  270 TYR cc_start: 0.8384 (t80) cc_final: 0.8061 (t80)
REVERT: A   48 LEU cc_start: 0.9478 (tp) cc_final: 0.9229 (tp)
REVERT: A   52 LEU cc_start: 0.9561 (mt) cc_final: 0.9334 (mt)
REVERT: A   79 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.8992 (ptm160)
REVERT: A   82 GLN cc_start: 0.9559 (tp40) cc_final: 0.9219 (mm-40)
REVERT: A   98 GLU cc_start: 0.9521 (mp0) cc_final: 0.9173 (pm20)
REVERT: A  100 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9111 (mm-30)
REVERT: A  104 LYS cc_start: 0.9515 (ttpp) cc_final: 0.9277 (mtmm)
REVERT: A  122 GLN cc_start: 0.8975 (pm20) cc_final: 0.8573 (pm20)
REVERT: A  151 HIS cc_start: 0.8597 (m90) cc_final: 0.8131 (m170)
REVERT: A  240 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8344 (mt-10)
REVERT: A  263 GLU cc_start: 0.8790 (pp20) cc_final: 0.8549 (pp20)
REVERT: A  268 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7576 (p0)
REVERT: A  269 TYR cc_start: 0.8515 (m-80) cc_final: 0.7820 (m-80)
  outliers start: 21
  outliers final: 16
  residues processed: 207
  average time/residue: 0.0542
  time to fit residues: 14.5523
Evaluate side-chains
  217 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 199
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  180 GLN
Chi-restraints excluded: chain A residue  217 PHE
Chi-restraints excluded: chain A residue  219 CYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0050
   chunk 44 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 12 optimal weight:    0.1980
   chunk 33 optimal weight:    0.0010
   chunk 10 optimal weight:    0.4980
   chunk 34 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.2800

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

Flipped N/Q/H residues before XYZ refinement:
A 180 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.153177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.102481 restraints weight = 7368.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 4.29
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4273  Z= 0.161
  Angle     :  0.838  12.749   5805  Z= 0.399
  Chirality :  0.044   0.241    688
  Planarity :  0.005   0.062    692
  Dihedral  :  5.736  51.935    611
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 33.71 %
    Favored  : 62.25 %
  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:  2.49 (0.36), residues: 522
  helix:  2.38 (0.24), residues: 410
  sheet:  None (None), residues: 0
  loop : -1.21 (0.58), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  79 
 TYR   0.020   0.002   TYR B  57 
 PHE   0.025   0.001   PHE A  51 
 TRP   0.013   0.001   TRP B  44 
 HIS   0.003   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 4272)
  covalent geometry    : angle       0.83835 ( 5803)
  SS BOND              : bond        0.00614 (    1)
  SS BOND              : angle       0.46299 (    2)
  hydrogen bonds       : bond        0.03962 (  334)
  hydrogen bonds       : angle       4.28590 ( 1002)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 208
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   95 GLN cc_start: 0.9164 (mp10) cc_final: 0.8950 (mp10)
REVERT: B  101 ASP cc_start: 0.9657 (t0) cc_final: 0.9227 (m-30)
REVERT: B  104 LYS cc_start: 0.9456 (ttmm) cc_final: 0.9154 (mtmm)
REVERT: B  195 MET cc_start: 0.4135 (ttp) cc_final: 0.3874 (tpp)
REVERT: B  231 GLN cc_start: 0.8909 (tt0) cc_final: 0.8175 (tt0)
REVERT: B  240 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7907 (pt0)
REVERT: B  270 TYR cc_start: 0.8339 (t80) cc_final: 0.8112 (t80)
REVERT: A   48 LEU cc_start: 0.9463 (tp) cc_final: 0.9217 (tp)
REVERT: A   52 LEU cc_start: 0.9557 (mt) cc_final: 0.9313 (mt)
REVERT: A   79 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.8995 (ptm160)
REVERT: A   82 GLN cc_start: 0.9557 (tp40) cc_final: 0.9202 (mm-40)
REVERT: A   98 GLU cc_start: 0.9469 (mp0) cc_final: 0.9256 (pm20)
REVERT: A  122 GLN cc_start: 0.8988 (pm20) cc_final: 0.8593 (pm20)
REVERT: A  151 HIS cc_start: 0.8580 (m90) cc_final: 0.7834 (m90)
REVERT: A  172 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8421 (t80)
REVERT: A  240 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8332 (mt-10)
REVERT: A  263 GLU cc_start: 0.8719 (pp20) cc_final: 0.8476 (pp20)
REVERT: A  268 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7495 (p0)
REVERT: A  269 TYR cc_start: 0.8492 (m-80) cc_final: 0.7763 (m-80)
  outliers start: 18
  outliers final: 14
  residues processed: 212
  average time/residue: 0.0550
  time to fit residues: 15.2383
Evaluate side-chains
  215 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 198
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   93 CYS
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  217 PHE
Chi-restraints excluded: chain A residue  219 CYS
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  282 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3963 r_free = 0.3963 target = 0.150138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.104712 restraints weight = 7380.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 4.02
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.5014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   4273  Z= 0.187
  Angle     :  0.865  12.290   5805  Z= 0.416
  Chirality :  0.045   0.295    688
  Planarity :  0.005   0.065    692
  Dihedral  :  5.838  50.730    611
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 33.71 %
    Favored  : 61.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.42 (0.36), residues: 522
  helix:  2.32 (0.24), residues: 410
  sheet:  None (None), residues: 0
  loop : -1.22 (0.57), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  79 
 TYR   0.013   0.002   TYR A 270 
 PHE   0.036   0.002   PHE A 196 
 TRP   0.011   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 4272)
  covalent geometry    : angle       0.86530 ( 5803)
  SS BOND              : bond        0.00374 (    1)
  SS BOND              : angle       0.22152 (    2)
  hydrogen bonds       : bond        0.03996 (  334)
  hydrogen bonds       : angle       4.40042 ( 1002)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 201
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 ARG cc_start: 0.9112 (mtp-110) cc_final: 0.8745 (ttp-110)
REVERT: B  101 ASP cc_start: 0.9610 (t0) cc_final: 0.9218 (m-30)
REVERT: B  104 LYS cc_start: 0.9511 (ttmm) cc_final: 0.9192 (mtmm)
REVERT: B  195 MET cc_start: 0.4279 (ttp) cc_final: 0.3929 (tpp)
REVERT: B  231 GLN cc_start: 0.8918 (tt0) cc_final: 0.8209 (tt0)
REVERT: B  240 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7946 (pt0)
REVERT: A   48 LEU cc_start: 0.9506 (tp) cc_final: 0.9296 (tp)
REVERT: A   52 LEU cc_start: 0.9573 (mt) cc_final: 0.9302 (mt)
REVERT: A   79 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.9112 (ptm160)
REVERT: A  122 GLN cc_start: 0.8946 (pm20) cc_final: 0.8572 (pm20)
REVERT: A  151 HIS cc_start: 0.8621 (m90) cc_final: 0.8195 (m170)
REVERT: A  207 ARG cc_start: 0.8611 (tmt170) cc_final: 0.8256 (tpt90)
REVERT: A  240 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8352 (mt-10)
REVERT: A  263 GLU cc_start: 0.8708 (pp20) cc_final: 0.8453 (pp20)
REVERT: A  268 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7506 (p0)
REVERT: A  269 TYR cc_start: 0.8460 (m-80) cc_final: 0.7760 (m-80)
  outliers start: 20
  outliers final: 16
  residues processed: 205
  average time/residue: 0.0543
  time to fit residues: 14.5960
Evaluate side-chains
  213 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 195
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   93 CYS
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  217 PHE
Chi-restraints excluded: chain A residue  219 CYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3973 r_free = 0.3973 target = 0.151000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.100152 restraints weight = 7538.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 4.34
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.5124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   4273  Z= 0.192
  Angle     :  0.912  12.346   5805  Z= 0.439
  Chirality :  0.046   0.325    688
  Planarity :  0.005   0.067    692
  Dihedral  :  5.865  51.360    611
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 34.83 %
    Favored  : 60.00 %
  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:  2.34 (0.36), residues: 522
  helix:  2.25 (0.24), residues: 409
  sheet:  None (None), residues: 0
  loop : -1.16 (0.57), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  79 
 TYR   0.022   0.002   TYR B 270 
 PHE   0.026   0.001   PHE A  51 
 TRP   0.011   0.001   TRP A 127 
 HIS   0.003   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 4272)
  covalent geometry    : angle       0.91176 ( 5803)
  SS BOND              : bond        0.00423 (    1)
  SS BOND              : angle       0.64507 (    2)
  hydrogen bonds       : bond        0.04009 (  334)
  hydrogen bonds       : angle       4.37284 ( 1002)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 203
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 ARG cc_start: 0.9196 (mtp-110) cc_final: 0.8902 (ttp-110)
REVERT: B   82 GLN cc_start: 0.9492 (mm110) cc_final: 0.9072 (tp40)
REVERT: B  101 ASP cc_start: 0.9618 (t0) cc_final: 0.9206 (m-30)
REVERT: B  104 LYS cc_start: 0.9510 (ttmm) cc_final: 0.9217 (mtmm)
REVERT: B  231 GLN cc_start: 0.8862 (tt0) cc_final: 0.8603 (tt0)
REVERT: B  240 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7933 (pt0)
REVERT: A   48 LEU cc_start: 0.9489 (tp) cc_final: 0.9278 (tp)
REVERT: A   52 LEU cc_start: 0.9559 (mt) cc_final: 0.9286 (mt)
REVERT: A   79 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.9124 (ptm160)
REVERT: A   98 GLU cc_start: 0.9379 (pm20) cc_final: 0.9059 (pm20)
REVERT: A  122 GLN cc_start: 0.9022 (pm20) cc_final: 0.8648 (pm20)
REVERT: A  151 HIS cc_start: 0.8617 (m90) cc_final: 0.8130 (m170)
REVERT: A  172 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8407 (t80)
REVERT: A  207 ARG cc_start: 0.8717 (tmt170) cc_final: 0.8446 (tpt90)
REVERT: A  240 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8337 (mt-10)
REVERT: A  263 GLU cc_start: 0.8852 (pp20) cc_final: 0.8603 (pp20)
REVERT: A  268 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7510 (p0)
REVERT: A  269 TYR cc_start: 0.8541 (m-80) cc_final: 0.7819 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 209
  average time/residue: 0.0549
  time to fit residues: 15.0876
Evaluate side-chains
  221 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 199
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   93 CYS
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  217 PHE
Chi-restraints excluded: chain A residue  219 CYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0050
   chunk 18 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.6194

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.150688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.100518 restraints weight = 7265.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 4.16
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.5260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   4273  Z= 0.185
  Angle     :  0.955  13.004   5805  Z= 0.457
  Chirality :  0.048   0.335    688
  Planarity :  0.005   0.065    692
  Dihedral  :  5.855  53.371    611
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 36.63 %
    Favored  : 59.10 %
  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:  2.21 (0.36), residues: 522
  helix:  2.16 (0.24), residues: 407
  sheet:  None (None), residues: 0
  loop : -1.17 (0.57), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  79 
 TYR   0.025   0.002   TYR B 270 
 PHE   0.027   0.002   PHE A  51 
 TRP   0.012   0.001   TRP A 127 
 HIS   0.004   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 4272)
  covalent geometry    : angle       0.95490 ( 5803)
  SS BOND              : bond        0.00340 (    1)
  SS BOND              : angle       0.30234 (    2)
  hydrogen bonds       : bond        0.04023 (  334)
  hydrogen bonds       : angle       4.47570 ( 1002)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 201
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 ARG cc_start: 0.9206 (mtp-110) cc_final: 0.8941 (ttp-110)
REVERT: B   82 GLN cc_start: 0.9487 (mm110) cc_final: 0.9080 (tp40)
REVERT: B  101 ASP cc_start: 0.9627 (t0) cc_final: 0.9213 (m-30)
REVERT: B  104 LYS cc_start: 0.9515 (ttmm) cc_final: 0.9220 (mtmm)
REVERT: B  240 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7939 (pt0)
REVERT: B  301 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8772 (ptpp)
REVERT: A   48 LEU cc_start: 0.9489 (tp) cc_final: 0.9277 (tp)
REVERT: A   52 LEU cc_start: 0.9566 (mt) cc_final: 0.9282 (mt)
REVERT: A   79 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.9137 (ptm160)
REVERT: A  122 GLN cc_start: 0.9014 (pm20) cc_final: 0.8669 (pm20)
REVERT: A  151 HIS cc_start: 0.8648 (m90) cc_final: 0.8171 (m170)
REVERT: A  196 PHE cc_start: 0.8981 (t80) cc_final: 0.8767 (t80)
REVERT: A  207 ARG cc_start: 0.8757 (tmt170) cc_final: 0.8488 (tpt90)
REVERT: A  240 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8319 (mt-10)
REVERT: A  263 GLU cc_start: 0.8718 (pp20) cc_final: 0.8441 (pp20)
REVERT: A  268 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7457 (p0)
REVERT: A  269 TYR cc_start: 0.8505 (m-80) cc_final: 0.7775 (m-80)
  outliers start: 19
  outliers final: 17
  residues processed: 205
  average time/residue: 0.0565
  time to fit residues: 15.1170
Evaluate side-chains
  217 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 198
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   93 CYS
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  217 PHE
Chi-restraints excluded: chain A residue  219 CYS
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.150307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.101057 restraints weight = 7332.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 4.17
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.5337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   4273  Z= 0.197
  Angle     :  0.967  12.710   5805  Z= 0.468
  Chirality :  0.048   0.333    688
  Planarity :  0.005   0.064    692
  Dihedral  :  5.927  54.942    611
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 37.08 %
    Favored  : 58.65 %
  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:  2.17 (0.36), residues: 522
  helix:  2.12 (0.24), residues: 404
  sheet:  None (None), residues: 0
  loop : -1.00 (0.56), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 297 
 TYR   0.024   0.002   TYR B 270 
 PHE   0.027   0.002   PHE A  51 
 TRP   0.011   0.001   TRP A 127 
 HIS   0.004   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 4272)
  covalent geometry    : angle       0.96689 ( 5803)
  SS BOND              : bond        0.00315 (    1)
  SS BOND              : angle       0.27296 (    2)
  hydrogen bonds       : bond        0.04092 (  334)
  hydrogen bonds       : angle       4.43845 ( 1002)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1027.30 seconds
wall clock time: 18 minutes 16.40 seconds (1096.40 seconds total)