Starting phenix.real_space_refine
on Fri Aug 22 18:18:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w9o_37377/08_2025/8w9o_37377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w9o_37377/08_2025/8w9o_37377.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w9o_37377/08_2025/8w9o_37377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w9o_37377/08_2025/8w9o_37377.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w9o_37377/08_2025/8w9o_37377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w9o_37377/08_2025/8w9o_37377.map"
  }
  resolution = 2.8
  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=   0.006
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       4      8.98       5
     S      40      5.16       5
     C    4570      2.51       5
     N    1058      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6862
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3429
          Classifications: {'peptide': 427}
          Link IDs: {'PTRANS': 13, 'TRANS': 413}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3429
          Classifications: {'peptide': 427}
          Link IDs: {'PTRANS': 13, 'TRANS': 413}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'  K': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'  K': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.09, per 1000 atoms: 0.30
  Number of scatterers: 6862
  At special positions: 0
  Unit cell: (103.23, 89.28, 85.56, 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       4     19.00
     S      40     16.00
     O    1190      8.00
     N    1058      7.00
     C    4570      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 449 " - pdb=" SG  CYS A 460 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 449 " - pdb=" SG  CYS B 460 " 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: 0.67
  Conformation dependent library (CDL) restraints added in 456.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1604

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 2 sheets defined
      72.7% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 43
    Processing helix  chain 'A' and resid 52 through 65
    Processing helix  chain 'A' and resid 78 through 93
    Processing helix  chain 'A' and resid 93 through 110
    Processing helix  chain 'A' and resid 149 through 183
    Processing helix  chain 'A' and resid 183 through 193
      removed outlier: 3.794A  pdb=" N   VAL A 189 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 210
    Processing helix  chain 'A' and resid 220 through 225
    Processing helix  chain 'A' and resid 227 through 242
      Proline residue:  A 236  - end of helix
    Processing helix  chain 'A' and resid 244 through 261
    Processing helix  chain 'A' and resid 265 through 270
    Processing helix  chain 'A' and resid 282 through 308
    Processing helix  chain 'A' and resid 318 through 334
      removed outlier: 3.617A  pdb=" N   LEU A 323 " --> pdb=" O   SER A 319 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ARG A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 346
    Processing helix  chain 'A' and resid 347 through 360
    Processing helix  chain 'A' and resid 398 through 414
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 426 through 440
    Processing helix  chain 'A' and resid 454 through 458
    Processing helix  chain 'A' and resid 466 through 471
    Processing helix  chain 'A' and resid 472 through 488
    Processing helix  chain 'B' and resid 22 through 43
    Processing helix  chain 'B' and resid 52 through 65
    Processing helix  chain 'B' and resid 78 through 93
    Processing helix  chain 'B' and resid 93 through 110
    Processing helix  chain 'B' and resid 149 through 183
    Processing helix  chain 'B' and resid 183 through 193
      removed outlier: 3.767A  pdb=" N   VAL B 189 " --> pdb=" O   THR B 185 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU B 190 " --> pdb=" O   ALA B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 210
    Processing helix  chain 'B' and resid 220 through 225
    Processing helix  chain 'B' and resid 227 through 242
      Proline residue:  B 236  - end of helix
    Processing helix  chain 'B' and resid 244 through 261
    Processing helix  chain 'B' and resid 265 through 270
    Processing helix  chain 'B' and resid 271 through 275
    Processing helix  chain 'B' and resid 282 through 308
    Processing helix  chain 'B' and resid 318 through 333
      removed outlier: 3.532A  pdb=" N   LEU B 323 " --> pdb=" O   SER B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 346
    Processing helix  chain 'B' and resid 347 through 360
    Processing helix  chain 'B' and resid 398 through 414
    Processing helix  chain 'B' and resid 414 through 421
      removed outlier: 3.539A  pdb=" N   GLN B 419 " --> pdb=" O   ARG B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 440
    Processing helix  chain 'B' and resid 454 through 458
    Processing helix  chain 'B' and resid 466 through 471
    Processing helix  chain 'B' and resid 472 through 488
    Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366
    Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 500

    448 hydrogen bonds defined for protein.
    1272 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: 1.15

  Time building geometry restraints manager: 0.90 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: 2004
        1.34 -     1.45: 1203
        1.45 -     1.57: 3761
        1.57 -     1.69: 0
        1.69 -     1.80: 64
  Bond restraints: 7032
  Sorted by residual:
  bond pdb=" CB  THR B  71 "
       pdb=" CG2 THR B  71 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.29e+00
  bond pdb=" CG  LYS A 184 "
       pdb=" CD  LYS A 184 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.23e+00
  bond pdb=" C   MET A 367 "
       pdb=" O   MET A 367 "
    ideal  model  delta    sigma   weight residual
    1.242  1.230  0.012 1.16e-02 7.43e+03 1.06e+00
  bond pdb=" CB  LYS A 184 "
       pdb=" CG  LYS A 184 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.01e+00
  bond pdb=" CG  LYS B 184 "
       pdb=" CD  LYS B 184 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.40e-01
  ... (remaining 7027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 9347
        1.54 -     3.07: 156
        3.07 -     4.61: 29
        4.61 -     6.15: 4
        6.15 -     7.69: 2
  Bond angle restraints: 9538
  Sorted by residual:
  angle pdb=" CB  LYS A 184 "
        pdb=" CG  LYS A 184 "
        pdb=" CD  LYS A 184 "
      ideal   model   delta    sigma   weight residual
     111.30  118.99   -7.69 2.30e+00 1.89e-01 1.12e+01
  angle pdb=" CB  LYS B 184 "
        pdb=" CG  LYS B 184 "
        pdb=" CD  LYS B 184 "
      ideal   model   delta    sigma   weight residual
     111.30  117.99   -6.69 2.30e+00 1.89e-01 8.45e+00
  angle pdb=" CA  TYR A 158 "
        pdb=" CB  TYR A 158 "
        pdb=" CG  TYR A 158 "
      ideal   model   delta    sigma   weight residual
     113.90  118.63   -4.73 1.80e+00 3.09e-01 6.91e+00
  angle pdb=" CA  TYR B 158 "
        pdb=" CB  TYR B 158 "
        pdb=" CG  TYR B 158 "
      ideal   model   delta    sigma   weight residual
     113.90  118.41   -4.51 1.80e+00 3.09e-01 6.29e+00
  angle pdb=" CA  GLU A 194 "
        pdb=" CB  GLU A 194 "
        pdb=" CG  GLU A 194 "
      ideal   model   delta    sigma   weight residual
     114.10  118.55   -4.45 2.00e+00 2.50e-01 4.95e+00
  ... (remaining 9533 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.36: 3560
       17.36 -    34.72: 387
       34.72 -    52.08: 111
       52.08 -    69.44: 9
       69.44 -    86.80: 7
  Dihedral angle restraints: 4074
    sinusoidal: 1584
      harmonic: 2490
  Sorted by residual:
  dihedral pdb=" CA  ARG A 334 "
           pdb=" C   ARG A 334 "
           pdb=" N   HIS A 335 "
           pdb=" CA  HIS A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.35   25.65     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  ARG B 334 "
           pdb=" C   ARG B 334 "
           pdb=" N   HIS B 335 "
           pdb=" CA  HIS B 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.75   25.25     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  THR B  65 "
           pdb=" C   THR B  65 "
           pdb=" N   VAL B  66 "
           pdb=" CA  VAL B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.41  -20.59     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 4071 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 618
       0.030 -    0.059: 354
       0.059 -    0.089: 105
       0.089 -    0.118: 38
       0.118 -    0.148: 9
  Chirality restraints: 1124
  Sorted by residual:
  chirality pdb=" CA  HIS B 335 "
            pdb=" N   HIS B 335 "
            pdb=" C   HIS B 335 "
            pdb=" CB  HIS B 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.48e-01
  chirality pdb=" CG  LEU B 323 "
            pdb=" CB  LEU B 323 "
            pdb=" CD1 LEU B 323 "
            pdb=" CD2 LEU B 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.87e-01
  chirality pdb=" CA  ILE B 195 "
            pdb=" N   ILE B 195 "
            pdb=" C   ILE B 195 "
            pdb=" CB  ILE B 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.86e-01
  ... (remaining 1121 not shown)

  Planarity restraints: 1150
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 158 "   -0.013 2.00e-02 2.50e+03   1.11e-02 2.48e+00
        pdb=" CG  TYR B 158 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 158 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 158 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 158 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 158 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 158 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 158 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 158 "    0.013 2.00e-02 2.50e+03   1.11e-02 2.48e+00
        pdb=" CG  TYR A 158 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 158 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 158 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 158 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 158 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 158 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 158 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 188 "    0.006 2.00e-02 2.50e+03   1.17e-02 1.38e+00
        pdb=" CG  ASP A 188 "   -0.020 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 188 "    0.007 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 188 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1147 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.80: 2007
        2.80 -     3.39: 7906
        3.39 -     3.97: 13899
        3.97 -     4.56: 20701
        4.56 -     5.14: 28082
  Nonbonded interactions: 72595
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 427 "
            pdb=" OG1 THR A 431 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   ALA B  39 "
            pdb=" OG1 THR B  43 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   LYS B 155 "
            pdb=" OG  SER B 159 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   ASN A 169 "
            pdb=" OG  SER A 173 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OD1 ASP A 150 "
            pdb=" OH  TYR A 267 "
     model   vdw
     2.267 3.040
  ... (remaining 72590 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 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:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.180
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:8.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
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      :  0.005   0.038   7034  Z= 0.200
  Angle     :  0.538   7.685   9542  Z= 0.290
  Chirality :  0.041   0.148   1124
  Planarity :  0.003   0.027   1150
  Dihedral  : 15.896  86.800   2464
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.41 %
    Favored  : 78.28 %
  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 aren not related in a simple way.
  whole:  0.95 (0.29), residues: 842
  helix:  1.39 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.68 (0.38), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  50 
 TYR   0.027   0.002   TYR B 158 
 PHE   0.014   0.002   PHE B  32 
 TRP   0.004   0.001   TRP B 232 
 HIS   0.006   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 7032)
  covalent geometry    : angle       0.53850 ( 9538)
  SS BOND              : bond        0.00286 (    2)
  SS BOND              : angle       0.43800 (    4)
  hydrogen bonds       : bond        0.20367 (  448)
  hydrogen bonds       : angle       7.13601 ( 1272)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 14
  residues processed: 117
  average time/residue: 0.5476
  time to fit residues: 67.7308
Evaluate side-chains
  113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  273 ASN
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  313 SER
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  444 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0050
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 211 ASN
A 220 ASN
A 237 GLN
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 300 GLN
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 440 ASN
B 101 ASN
B 211 ASN
B 220 ASN
B 237 GLN
B 300 GLN
B 332 ASN
** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 GLN
B 426 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.150864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.131725 restraints weight = 8562.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.67
r_work: 0.3347 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7034  Z= 0.123
  Angle     :  0.490   5.868   9542  Z= 0.267
  Chirality :  0.039   0.138   1124
  Planarity :  0.004   0.030   1150
  Dihedral  :  5.396  47.765    940
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.61 %
    Favored  : 79.31 %
  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 aren not related in a simple way.
  whole:  1.58 (0.29), residues: 842
  helix:  1.82 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -0.54 (0.42), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 334 
 TYR   0.026   0.002   TYR A 158 
 PHE   0.015   0.001   PHE A 408 
 TRP   0.003   0.001   TRP A 232 
 HIS   0.003   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7032)
  covalent geometry    : angle       0.49056 ( 9538)
  SS BOND              : bond        0.00175 (    2)
  SS BOND              : angle       0.06406 (    4)
  hydrogen bonds       : bond        0.04229 (  448)
  hydrogen bonds       : angle       4.67948 ( 1272)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.6062 (mptt) cc_final: 0.5550 (tttt)
REVERT: A  248 PHE cc_start: 0.7944 (m-80) cc_final: 0.7617 (m-80)
REVERT: A  343 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7896 (mp)
REVERT: A  416 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7255 (mm110)
REVERT: B  220 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7155 (t0)
REVERT: B  315 GLU cc_start: 0.6250 (pm20) cc_final: 0.6034 (pm20)
REVERT: B  417 ASN cc_start: 0.7440 (m-40) cc_final: 0.7171 (m-40)
  outliers start: 24
  outliers final: 3
  residues processed: 130
  average time/residue: 0.5089
  time to fit residues: 70.3371
Evaluate side-chains
  110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  416 GLN
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  302 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 83 optimal weight:    0.0970
   chunk 11 optimal weight:    7.9990
   chunk 5 optimal weight:    0.4980
   chunk 48 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    1.4782

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 237 GLN
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN
B 101 ASN
B 220 ASN
B 237 GLN
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 335 HIS
B 416 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.148496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.129235 restraints weight = 8565.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.67
r_work: 0.3313 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7034  Z= 0.165
  Angle     :  0.504   6.021   9542  Z= 0.274
  Chirality :  0.040   0.140   1124
  Planarity :  0.004   0.028   1150
  Dihedral  :  4.572  47.193    918
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 19.02 %
    Favored  : 77.76 %
  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 aren not related in a simple way.
  whole:  1.56 (0.29), residues: 842
  helix:  1.79 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -0.51 (0.42), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 262 
 TYR   0.024   0.002   TYR A 158 
 PHE   0.014   0.001   PHE A 408 
 TRP   0.004   0.001   TRP B 232 
 HIS   0.004   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 7032)
  covalent geometry    : angle       0.50396 ( 9538)
  SS BOND              : bond        0.00365 (    2)
  SS BOND              : angle       0.36842 (    4)
  hydrogen bonds       : bond        0.04184 (  448)
  hydrogen bonds       : angle       4.50121 ( 1272)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.6127 (mptt) cc_final: 0.5651 (tttt)
REVERT: A  248 PHE cc_start: 0.7950 (m-80) cc_final: 0.7530 (m-80)
REVERT: A  343 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7956 (mp)
REVERT: A  416 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7186 (mm-40)
REVERT: B  152 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5570 (ttp80)
REVERT: B  315 GLU cc_start: 0.6359 (pm20) cc_final: 0.6086 (pm20)
REVERT: B  417 ASN cc_start: 0.7451 (m-40) cc_final: 0.7185 (m-40)
  outliers start: 25
  outliers final: 9
  residues processed: 118
  average time/residue: 0.4704
  time to fit residues: 59.0315
Evaluate side-chains
  114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  416 GLN
Chi-restraints excluded: chain B residue  152 ARG
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  396 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 237 GLN
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN
B 101 ASN
** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 GLN
B 332 ASN
B 416 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.151024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.132003 restraints weight = 8639.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.65
r_work: 0.3342 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7034  Z= 0.124
  Angle     :  0.470   7.123   9542  Z= 0.254
  Chirality :  0.039   0.172   1124
  Planarity :  0.003   0.028   1150
  Dihedral  :  4.440  46.669    918
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.64 %
    Favored  : 77.89 %
  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 aren not related in a simple way.
  whole:  1.76 (0.29), residues: 842
  helix:  1.95 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -0.46 (0.42), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 262 
 TYR   0.019   0.002   TYR B 158 
 PHE   0.014   0.001   PHE A 408 
 TRP   0.004   0.001   TRP B 232 
 HIS   0.003   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7032)
  covalent geometry    : angle       0.47001 ( 9538)
  SS BOND              : bond        0.00288 (    2)
  SS BOND              : angle       0.34434 (    4)
  hydrogen bonds       : bond        0.03701 (  448)
  hydrogen bonds       : angle       4.29321 ( 1272)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.6033 (OUTLIER) cc_final: 0.5619 (tttt)
REVERT: A  248 PHE cc_start: 0.7985 (m-80) cc_final: 0.7560 (m-80)
REVERT: A  343 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7928 (mp)
REVERT: A  416 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7169 (mm-40)
REVERT: B  315 GLU cc_start: 0.6372 (pm20) cc_final: 0.6069 (pm20)
REVERT: B  417 ASN cc_start: 0.7477 (m-40) cc_final: 0.7184 (m-40)
  outliers start: 27
  outliers final: 5
  residues processed: 125
  average time/residue: 0.4217
  time to fit residues: 55.9372
Evaluate side-chains
  115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  416 GLN
Chi-restraints excluded: chain B residue  343 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 220 ASN
A 237 GLN
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 101 ASN
** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 GLN
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.149682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.130357 restraints weight = 8547.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.66
r_work: 0.3330 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7034  Z= 0.138
  Angle     :  0.481   5.571   9542  Z= 0.259
  Chirality :  0.039   0.140   1124
  Planarity :  0.003   0.028   1150
  Dihedral  :  4.181  20.839    916
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.64 %
    Favored  : 77.63 %
  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 aren not related in a simple way.
  whole:  1.83 (0.29), residues: 842
  helix:  2.00 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -0.43 (0.42), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 334 
 TYR   0.021   0.002   TYR B 158 
 PHE   0.014   0.001   PHE A 408 
 TRP   0.004   0.001   TRP B 232 
 HIS   0.003   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7032)
  covalent geometry    : angle       0.48076 ( 9538)
  SS BOND              : bond        0.00342 (    2)
  SS BOND              : angle       0.41127 (    4)
  hydrogen bonds       : bond        0.03716 (  448)
  hydrogen bonds       : angle       4.27593 ( 1272)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5609 (tttt)
REVERT: A  248 PHE cc_start: 0.7969 (m-80) cc_final: 0.7442 (m-80)
REVERT: A  343 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7949 (mp)
REVERT: A  416 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7160 (mm-40)
REVERT: B  257 TYR cc_start: 0.6394 (t80) cc_final: 0.6048 (t80)
REVERT: B  315 GLU cc_start: 0.6448 (pm20) cc_final: 0.6183 (pm20)
REVERT: B  417 ASN cc_start: 0.7481 (m-40) cc_final: 0.7181 (m-40)
  outliers start: 29
  outliers final: 11
  residues processed: 126
  average time/residue: 0.4501
  time to fit residues: 60.2534
Evaluate side-chains
  118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  416 GLN
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  401 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 101 ASN
** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 GLN
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.151933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.132787 restraints weight = 8608.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.66
r_work: 0.3380 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7034  Z= 0.119
  Angle     :  0.464   5.309   9542  Z= 0.250
  Chirality :  0.039   0.137   1124
  Planarity :  0.003   0.028   1150
  Dihedral  :  4.085  19.434    916
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 19.28 %
    Favored  : 77.38 %
  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 aren not related in a simple way.
  whole:  1.97 (0.30), residues: 842
  helix:  2.11 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -0.38 (0.42), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 334 
 TYR   0.019   0.002   TYR B 158 
 PHE   0.013   0.001   PHE A 408 
 TRP   0.004   0.001   TRP B 232 
 HIS   0.003   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7032)
  covalent geometry    : angle       0.46436 ( 9538)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.33528 (    4)
  hydrogen bonds       : bond        0.03486 (  448)
  hydrogen bonds       : angle       4.18112 ( 1272)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.5911 (OUTLIER) cc_final: 0.5556 (tttt)
REVERT: A  248 PHE cc_start: 0.7928 (m-80) cc_final: 0.7449 (m-80)
REVERT: A  343 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7908 (mp)
REVERT: A  416 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7127 (mm-40)
REVERT: B  257 TYR cc_start: 0.6485 (t80) cc_final: 0.6137 (t80)
REVERT: B  315 GLU cc_start: 0.6507 (pm20) cc_final: 0.6249 (pm20)
REVERT: B  417 ASN cc_start: 0.7473 (m-40) cc_final: 0.7177 (m-40)
  outliers start: 26
  outliers final: 12
  residues processed: 130
  average time/residue: 0.4475
  time to fit residues: 61.7700
Evaluate side-chains
  120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  416 GLN
Chi-restraints excluded: chain B residue  158 TYR
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  401 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 79 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 3 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 101 ASN
B 220 ASN
B 237 GLN
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.150342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.130928 restraints weight = 8556.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.66
r_work: 0.3342 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7034  Z= 0.145
  Angle     :  0.492   7.328   9542  Z= 0.263
  Chirality :  0.040   0.207   1124
  Planarity :  0.003   0.028   1150
  Dihedral  :  4.170  20.185    916
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.41 %
    Favored  : 77.12 %
  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 aren not related in a simple way.
  whole:  1.90 (0.30), residues: 842
  helix:  2.05 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -0.39 (0.42), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 334 
 TYR   0.022   0.002   TYR B 158 
 PHE   0.013   0.001   PHE A 408 
 TRP   0.003   0.001   TRP B 232 
 HIS   0.003   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7032)
  covalent geometry    : angle       0.49179 ( 9538)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       0.45359 (    4)
  hydrogen bonds       : bond        0.03651 (  448)
  hydrogen bonds       : angle       4.24208 ( 1272)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5584 (tttt)
REVERT: A  194 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6227 (pm20)
REVERT: A  248 PHE cc_start: 0.7942 (m-80) cc_final: 0.7414 (m-80)
REVERT: A  343 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7932 (mp)
REVERT: A  416 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7137 (mm-40)
REVERT: B  257 TYR cc_start: 0.6564 (t80) cc_final: 0.6247 (t80)
REVERT: B  315 GLU cc_start: 0.6532 (pm20) cc_final: 0.6266 (pm20)
REVERT: B  417 ASN cc_start: 0.7475 (m-40) cc_final: 0.7171 (m-40)
  outliers start: 27
  outliers final: 14
  residues processed: 127
  average time/residue: 0.3970
  time to fit residues: 53.6203
Evaluate side-chains
  123 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  416 GLN
Chi-restraints excluded: chain B residue  158 TYR
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  401 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 80 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0270
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6842

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 101 ASN
B 237 GLN
B 332 ASN
B 416 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.152285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.132869 restraints weight = 8641.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.68
r_work: 0.3358 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7034  Z= 0.111
  Angle     :  0.481   8.793   9542  Z= 0.255
  Chirality :  0.039   0.236   1124
  Planarity :  0.003   0.030   1150
  Dihedral  :  4.030  19.246    916
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.05 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.30), residues: 842
  helix:  2.14 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -0.33 (0.42), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 334 
 TYR   0.017   0.002   TYR B 158 
 PHE   0.013   0.001   PHE A 408 
 TRP   0.004   0.000   TRP B 232 
 HIS   0.004   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 7032)
  covalent geometry    : angle       0.48138 ( 9538)
  SS BOND              : bond        0.00265 (    2)
  SS BOND              : angle       0.27967 (    4)
  hydrogen bonds       : bond        0.03353 (  448)
  hydrogen bonds       : angle       4.14160 ( 1272)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5421 (tttt)
REVERT: A  248 PHE cc_start: 0.7853 (m-80) cc_final: 0.7371 (m-80)
REVERT: A  343 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7860 (mp)
REVERT: A  416 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7130 (mm-40)
REVERT: B  315 GLU cc_start: 0.6509 (pm20) cc_final: 0.6239 (pm20)
REVERT: B  334 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.7368 (mmm-85)
REVERT: B  417 ASN cc_start: 0.7453 (m-40) cc_final: 0.7154 (m-40)
  outliers start: 24
  outliers final: 14
  residues processed: 128
  average time/residue: 0.4454
  time to fit residues: 60.6326
Evaluate side-chains
  124 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  416 GLN
Chi-restraints excluded: chain B residue  158 TYR
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  401 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 3 optimal weight:    0.3980
   chunk 60 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 101 ASN
B 237 GLN
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.152544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.133138 restraints weight = 8624.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.68
r_work: 0.3374 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7034  Z= 0.112
  Angle     :  0.476   8.074   9542  Z= 0.253
  Chirality :  0.039   0.175   1124
  Planarity :  0.003   0.030   1150
  Dihedral  :  4.016  19.002    916
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.44 %
    Favored  : 76.74 %
  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 aren not related in a simple way.
  whole:  2.06 (0.30), residues: 842
  helix:  2.16 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -0.31 (0.43), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 334 
 TYR   0.018   0.002   TYR B 158 
 PHE   0.013   0.001   PHE A 408 
 TRP   0.004   0.000   TRP A 232 
 HIS   0.004   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 7032)
  covalent geometry    : angle       0.47622 ( 9538)
  SS BOND              : bond        0.00139 (    2)
  SS BOND              : angle       0.26003 (    4)
  hydrogen bonds       : bond        0.03329 (  448)
  hydrogen bonds       : angle       4.11377 ( 1272)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.5783 (OUTLIER) cc_final: 0.5432 (tttt)
REVERT: A  343 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7881 (mp)
REVERT: A  416 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7067 (mm-40)
REVERT: B  315 GLU cc_start: 0.6477 (pm20) cc_final: 0.6230 (pm20)
REVERT: B  417 ASN cc_start: 0.7462 (m-40) cc_final: 0.7095 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 124
  average time/residue: 0.4622
  time to fit residues: 61.1022
Evaluate side-chains
  125 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  416 GLN
Chi-restraints excluded: chain B residue  158 TYR
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  401 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 242 ASN
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 335 HIS
B 101 ASN
B 237 GLN
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.150559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.131249 restraints weight = 8464.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.65
r_work: 0.3329 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7034  Z= 0.153
  Angle     :  0.511   7.690   9542  Z= 0.272
  Chirality :  0.040   0.170   1124
  Planarity :  0.004   0.028   1150
  Dihedral  :  4.194  20.426    916
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.44 %
    Favored  : 76.48 %
  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 aren not related in a simple way.
  whole:  1.87 (0.30), residues: 842
  helix:  2.01 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -0.38 (0.42), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 334 
 TYR   0.022   0.002   TYR B 158 
 PHE   0.013   0.001   PHE A 408 
 TRP   0.004   0.001   TRP B 499 
 HIS   0.003   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 7032)
  covalent geometry    : angle       0.51126 ( 9538)
  SS BOND              : bond        0.00176 (    2)
  SS BOND              : angle       0.47273 (    4)
  hydrogen bonds       : bond        0.03688 (  448)
  hydrogen bonds       : angle       4.24063 ( 1272)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.5801 (OUTLIER) cc_final: 0.5455 (tttt)
REVERT: A  248 PHE cc_start: 0.7908 (m-80) cc_final: 0.7401 (m-80)
REVERT: A  343 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7938 (mp)
REVERT: A  416 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7144 (mm-40)
REVERT: B  315 GLU cc_start: 0.6560 (pm20) cc_final: 0.6270 (pm20)
REVERT: B  417 ASN cc_start: 0.7445 (m-40) cc_final: 0.7176 (m-40)
  outliers start: 24
  outliers final: 16
  residues processed: 122
  average time/residue: 0.5084
  time to fit residues: 65.8643
Evaluate side-chains
  124 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  416 GLN
Chi-restraints excluded: chain B residue  158 TYR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  401 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 64 optimal weight:    6.9990
   chunk 46 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN
B 101 ASN
B 237 GLN
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.153205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.133963 restraints weight = 8577.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.66
r_work: 0.3385 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7034  Z= 0.115
  Angle     :  0.484   7.894   9542  Z= 0.258
  Chirality :  0.039   0.170   1124
  Planarity :  0.003   0.028   1150
  Dihedral  :  4.036  19.434    916
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 20.44 %
    Favored  : 76.61 %
  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 aren not related in a simple way.
  whole:  2.02 (0.30), residues: 842
  helix:  2.14 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -0.33 (0.42), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 152 
 TYR   0.018   0.002   TYR B 158 
 PHE   0.013   0.001   PHE A 408 
 TRP   0.003   0.000   TRP B 232 
 HIS   0.003   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7032)
  covalent geometry    : angle       0.48403 ( 9538)
  SS BOND              : bond        0.00132 (    2)
  SS BOND              : angle       0.29801 (    4)
  hydrogen bonds       : bond        0.03390 (  448)
  hydrogen bonds       : angle       4.15128 ( 1272)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2201.12 seconds
wall clock time: 38 minutes 34.99 seconds (2314.99 seconds total)