Starting phenix.real_space_refine
on Fri Aug 22 15:12:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8omu_16977/08_2025/8omu_16977.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8omu_16977/08_2025/8omu_16977.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8omu_16977/08_2025/8omu_16977.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8omu_16977/08_2025/8omu_16977.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8omu_16977/08_2025/8omu_16977.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8omu_16977/08_2025/8omu_16977.cif"
  }
  resolution = 3.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.060
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    3064      2.51       5
     N     804      2.21       5
     O     834      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  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: 4737
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3842
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 25, 'TRANS': 471}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 895
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
  Time building chain proxies: 1.19, per 1000 atoms: 0.25
  Number of scatterers: 4737
  At special positions: 0
  Unit cell: (117.312, 68.224, 81.536, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O     834      8.00
     N     804      7.00
     C    3064      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 105 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A 128 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " 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: 0.40
  Conformation dependent library (CDL) restraints added in 181.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1124

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 4 sheets defined
      64.7% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.856A  pdb=" N   LEU A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 24
      removed outlier: 3.533A  pdb=" N   LEU A  18 " --> pdb=" O   GLY A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 37
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 56 through 61
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 132 through 160
      removed outlier: 3.955A  pdb=" N   PHE A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   TYR A 154 " --> pdb=" O   MET A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 181
    Processing helix  chain 'A' and resid 184 through 214
      removed outlier: 4.144A  pdb=" N   MET A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   THR A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 244
      removed outlier: 3.592A  pdb=" N   ALA A 238 " --> pdb=" O   GLN A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 265
      removed outlier: 3.847A  pdb=" N   LEU A 252 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      Proline residue:  A 257  - end of helix
      removed outlier: 3.624A  pdb=" N   ILE A 260 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 268
      No H-bonds generated for 'chain 'A' and resid 266 through 268'
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 281 through 296
    Processing helix  chain 'A' and resid 297 through 303
      removed outlier: 3.576A  pdb=" N   GLY A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LYS A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 313
    Processing helix  chain 'A' and resid 326 through 332
    Processing helix  chain 'A' and resid 332 through 358
    Processing helix  chain 'A' and resid 366 through 392
      removed outlier: 4.259A  pdb=" N   LEU A 379 " --> pdb=" O   GLY A 375 " (cutoff:3.500A)
      Proline residue:  A 380  - end of helix
    Processing helix  chain 'A' and resid 394 through 415
      removed outlier: 3.543A  pdb=" N   LEU A 404 " --> pdb=" O   ALA A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 447
    Processing helix  chain 'A' and resid 453 through 477
      Proline residue:  A 473  - end of helix
    Processing helix  chain 'A' and resid 478 through 481
    Processing helix  chain 'A' and resid 484 through 501
      Proline residue:  A 494  - end of helix
    Processing helix  chain 'A' and resid 515 through 525
      removed outlier: 3.574A  pdb=" N   ARG A 524 " --> pdb=" O   LYS A 520 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLY A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 56
      removed outlier: 4.298A  pdb=" N   SER B  56 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 53 through 56'
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 4.238A  pdb=" N   THR B  91 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80
    Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 7
      removed outlier: 3.575A  pdb=" N   LEU B  20 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL B  79 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   THR B  69 " --> pdb=" O   GLN B  82 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.386A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 112 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR B 109 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA B  92 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ALA B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)

    289 hydrogen bonds defined for protein.
    849 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.57

  Time building geometry restraints manager: 0.53 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: 1491
        1.34 -     1.46: 1127
        1.46 -     1.58: 2178
        1.58 -     1.70: 0
        1.70 -     1.82: 55
  Bond restraints: 4851
  Sorted by residual:
  bond pdb=" CA  GLN A 510 "
       pdb=" CB  GLN A 510 "
    ideal  model  delta    sigma   weight residual
    1.522  1.531 -0.008 7.00e-03 2.04e+04 1.44e+00
  bond pdb=" C   SER B 114 "
       pdb=" O   SER B 114 "
    ideal  model  delta    sigma   weight residual
    1.242  1.231  0.010 1.00e-02 1.00e+04 1.02e+00
  bond pdb=" CB  CYS A 385 "
       pdb=" SG  CYS A 385 "
    ideal  model  delta    sigma   weight residual
    1.808  1.776  0.032 3.30e-02 9.18e+02 9.48e-01
  bond pdb=" CA  THR A  36 "
       pdb=" C   THR A  36 "
    ideal  model  delta    sigma   weight residual
    1.522  1.535 -0.013 1.37e-02 5.33e+03 8.51e-01
  bond pdb=" C   MET A 485 "
       pdb=" N   PRO A 486 "
    ideal  model  delta    sigma   weight residual
    1.335  1.347 -0.012 1.36e-02 5.41e+03 7.79e-01
  ... (remaining 4846 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 6489
        2.11 -     4.23: 87
        4.23 -     6.34: 12
        6.34 -     8.45: 6
        8.45 -    10.56: 2
  Bond angle restraints: 6596
  Sorted by residual:
  angle pdb=" O   SER B 114 "
        pdb=" C   SER B 114 "
        pdb=" N   ALA B 115 "
      ideal   model   delta    sigma   weight residual
     121.20  113.31    7.89 1.61e+00 3.86e-01 2.40e+01
  angle pdb=" CA  LYS A 297 "
        pdb=" CB  LYS A 297 "
        pdb=" CG  LYS A 297 "
      ideal   model   delta    sigma   weight residual
     114.10  121.59   -7.49 2.00e+00 2.50e-01 1.40e+01
  angle pdb=" CA  GLN B  39 "
        pdb=" CB  GLN B  39 "
        pdb=" CG  GLN B  39 "
      ideal   model   delta    sigma   weight residual
     114.10  121.02   -6.92 2.00e+00 2.50e-01 1.20e+01
  angle pdb=" CB  MET A 464 "
        pdb=" CG  MET A 464 "
        pdb=" SD  MET A 464 "
      ideal   model   delta    sigma   weight residual
     112.70  122.76  -10.06 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" CA  LEU A  18 "
        pdb=" CB  LEU A  18 "
        pdb=" CG  LEU A  18 "
      ideal   model   delta    sigma   weight residual
     116.30  126.86  -10.56 3.50e+00 8.16e-02 9.11e+00
  ... (remaining 6591 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 2367
       17.39 -    34.78: 352
       34.78 -    52.17: 115
       52.17 -    69.56: 14
       69.56 -    86.95: 7
  Dihedral angle restraints: 2855
    sinusoidal: 1097
      harmonic: 1758
  Sorted by residual:
  dihedral pdb=" CB  CYS A  49 "
           pdb=" SG  CYS A  49 "
           pdb=" SG  CYS A 105 "
           pdb=" CB  CYS A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.51   54.51     1      1.00e+01 1.00e-02 4.03e+01
  dihedral pdb=" CB  CYS A  78 "
           pdb=" SG  CYS A  78 "
           pdb=" SG  CYS A 128 "
           pdb=" CB  CYS A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -47.78  -38.22     1      1.00e+01 1.00e-02 2.06e+01
  dihedral pdb=" CA  CYS A  49 "
           pdb=" CB  CYS A  49 "
           pdb=" SG  CYS A  49 "
           pdb=" SG  CYS A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00   -6.88  -66.12     1      2.00e+01 2.50e-03 1.43e+01
  ... (remaining 2852 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 435
       0.026 -    0.053: 191
       0.053 -    0.079: 75
       0.079 -    0.106: 42
       0.106 -    0.132: 12
  Chirality restraints: 755
  Sorted by residual:
  chirality pdb=" CA  ASN A 125 "
            pdb=" N   ASN A 125 "
            pdb=" C   ASN A 125 "
            pdb=" CB  ASN A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.37e-01
  chirality pdb=" CA  ILE A  44 "
            pdb=" N   ILE A  44 "
            pdb=" C   ILE A  44 "
            pdb=" CB  ILE A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.97e-01
  chirality pdb=" CG  LEU A 434 "
            pdb=" CB  LEU A 434 "
            pdb=" CD1 LEU A 434 "
            pdb=" CD2 LEU A 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.47   -0.12 2.00e-01 2.50e+01 3.87e-01
  ... (remaining 752 not shown)

  Planarity restraints: 824
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 114 "    0.043 2.00e-02 2.50e+03   8.02e-02 6.43e+01
        pdb=" C   SER B 114 "   -0.139 2.00e-02 2.50e+03
        pdb=" O   SER B 114 "    0.050 2.00e-02 2.50e+03
        pdb=" N   ALA B 115 "    0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 220 "   -0.010 2.00e-02 2.50e+03   2.10e-02 4.40e+00
        pdb=" C   ALA A 220 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ALA A 220 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   TYR A 221 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  36 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.58e+00
        pdb=" C   THR A  36 "    0.033 2.00e-02 2.50e+03
        pdb=" O   THR A  36 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A  37 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 821 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 886
        2.76 -     3.30: 4667
        3.30 -     3.83: 8318
        3.83 -     4.37: 8848
        4.37 -     4.90: 15563
  Nonbonded interactions: 38282
  Sorted by model distance:
  nonbonded pdb=" O   MET A  23 "
            pdb=" OH  TYR A 264 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   PHE A 133 "
            pdb=" OH  TYR A 185 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG1 THR A 451 "
            pdb=" OD1 ASP A 514 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OE1 GLU B  35 "
            pdb=" OH  TYR B  37 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   LYS A 520 "
            pdb=" OG  SER A 523 "
     model   vdw
     2.358 3.040
  ... (remaining 38277 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.360
  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:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.500
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
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      :  0.003   0.032   4854  Z= 0.142
  Angle     :  0.650  10.565   6602  Z= 0.329
  Chirality :  0.040   0.132    755
  Planarity :  0.005   0.080    824
  Dihedral  : 18.005  86.945   1722
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 35.56 %
    Favored  : 63.65 %
  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 aren not related in a simple way.
  whole:  0.64 (0.36), residues: 604
  helix:  1.35 (0.29), residues: 355
  sheet: -1.36 (0.75), residues: 42
  loop : -0.73 (0.46), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 273 
 TYR   0.022   0.001   TYR A 354 
 PHE   0.012   0.001   PHE A 351 
 TRP   0.008   0.001   TRP A 346 
 HIS   0.002   0.000   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4851)
  covalent geometry    : angle       0.64981 ( 6596)
  SS BOND              : bond        0.00445 (    3)
  SS BOND              : angle       0.55438 (    6)
  hydrogen bonds       : bond        0.14994 (  289)
  hydrogen bonds       : angle       5.65273 (  849)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.121 
Fit side-chains
REVERT: B   29 VAL cc_start: 0.5845 (OUTLIER) cc_final: 0.5645 (m)
REVERT: B   90 ASP cc_start: 0.7781 (m-30) cc_final: 0.7430 (m-30)
  outliers start: 4
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0682
  time to fit residues: 6.5806
Evaluate side-chains
  74 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4398 r_free = 0.4398 target = 0.209260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.172223 restraints weight = 6186.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 2.32
r_work: 0.3888 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.0662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4854  Z= 0.144
  Angle     :  0.607   8.530   6602  Z= 0.313
  Chirality :  0.040   0.135    755
  Planarity :  0.004   0.029    824
  Dihedral  :  4.068  18.929    668
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 31.24 %
    Favored  : 64.44 %
  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:  0.78 (0.36), residues: 604
  helix:  1.34 (0.28), residues: 360
  sheet: -1.19 (0.76), residues: 42
  loop : -0.49 (0.47), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 273 
 TYR   0.021   0.001   TYR A 354 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4851)
  covalent geometry    : angle       0.60650 ( 6596)
  SS BOND              : bond        0.00443 (    3)
  SS BOND              : angle       0.75123 (    6)
  hydrogen bonds       : bond        0.04470 (  289)
  hydrogen bonds       : angle       4.71964 (  849)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.107 
Fit side-chains
REVERT: B   90 ASP cc_start: 0.7760 (m-30) cc_final: 0.7092 (m-30)
  outliers start: 22
  outliers final: 13
  residues processed: 99
  average time/residue: 0.0664
  time to fit residues: 8.5869
Evaluate side-chains
  87 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLN
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain B residue  102 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4372 r_free = 0.4372 target = 0.206127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.170028 restraints weight = 6158.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 2.20
r_work: 0.3924 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3778 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.0849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4854  Z= 0.141
  Angle     :  0.589   8.681   6602  Z= 0.301
  Chirality :  0.040   0.133    755
  Planarity :  0.004   0.028    824
  Dihedral  :  3.948  17.495    667
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 29.27 %
    Favored  : 64.83 %
  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:  0.81 (0.36), residues: 604
  helix:  1.31 (0.28), residues: 361
  sheet: -1.11 (0.79), residues: 42
  loop : -0.40 (0.47), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 273 
 TYR   0.019   0.001   TYR A 354 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.008   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4851)
  covalent geometry    : angle       0.58884 ( 6596)
  SS BOND              : bond        0.00430 (    3)
  SS BOND              : angle       0.62399 (    6)
  hydrogen bonds       : bond        0.04206 (  289)
  hydrogen bonds       : angle       4.59036 (  849)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8257 (ttp80)
REVERT: B   82 GLN cc_start: 0.6289 (pp30) cc_final: 0.5676 (tm-30)
REVERT: B   90 ASP cc_start: 0.7824 (m-30) cc_final: 0.7466 (m-30)
  outliers start: 30
  outliers final: 19
  residues processed: 103
  average time/residue: 0.0661
  time to fit residues: 8.6858
Evaluate side-chains
  97 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLN
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain B residue  102 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0370
   chunk 17 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.206442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.170483 restraints weight = 6234.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 2.24
r_work: 0.3919 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.1043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4854  Z= 0.130
  Angle     :  0.588   9.592   6602  Z= 0.296
  Chirality :  0.040   0.135    755
  Planarity :  0.004   0.031    824
  Dihedral  :  3.914  17.682    667
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 29.47 %
    Favored  : 64.44 %
  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:  0.94 (0.36), residues: 604
  helix:  1.42 (0.28), residues: 361
  sheet: -0.94 (0.81), residues: 42
  loop : -0.37 (0.47), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 273 
 TYR   0.019   0.001   TYR A 354 
 PHE   0.012   0.001   PHE A 351 
 TRP   0.008   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4851)
  covalent geometry    : angle       0.58776 ( 6596)
  SS BOND              : bond        0.00324 (    3)
  SS BOND              : angle       0.60405 (    6)
  hydrogen bonds       : bond        0.03969 (  289)
  hydrogen bonds       : angle       4.51349 (  849)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 86
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ARG cc_start: 0.8310 (ttp80) cc_final: 0.8027 (ttp80)
REVERT: B   90 ASP cc_start: 0.7650 (m-30) cc_final: 0.7284 (m-30)
  outliers start: 31
  outliers final: 22
  residues processed: 114
  average time/residue: 0.0600
  time to fit residues: 9.0007
Evaluate side-chains
  99 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   17 GLN
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  102 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 43 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B   1 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.208438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.172242 restraints weight = 6180.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 2.25
r_work: 0.3907 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.1140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4854  Z= 0.139
  Angle     :  0.600  10.047   6602  Z= 0.301
  Chirality :  0.040   0.130    755
  Planarity :  0.004   0.034    824
  Dihedral  :  3.925  17.581    667
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 28.68 %
    Favored  : 65.03 %
  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 (0.36), residues: 604
  helix:  1.41 (0.28), residues: 361
  sheet: -0.89 (0.81), residues: 42
  loop : -0.34 (0.48), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 273 
 TYR   0.019   0.001   TYR A 354 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.008   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4851)
  covalent geometry    : angle       0.59982 ( 6596)
  SS BOND              : bond        0.00713 (    3)
  SS BOND              : angle       0.95603 (    6)
  hydrogen bonds       : bond        0.04048 (  289)
  hydrogen bonds       : angle       4.49766 (  849)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 82
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A   80 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8046 (ttp80)
REVERT: B   90 ASP cc_start: 0.7566 (m-30) cc_final: 0.7217 (m-30)
  outliers start: 32
  outliers final: 26
  residues processed: 110
  average time/residue: 0.0570
  time to fit residues: 8.3147
Evaluate side-chains
  105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   17 GLN
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain B residue    5 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 27 optimal weight:    0.1980
   chunk 19 optimal weight:    0.1980
   chunk 59 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.4382 r_free = 0.4382 target = 0.207421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.171604 restraints weight = 6259.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.4039 rms_B_bonded: 2.25
r_work: 0.3935 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3786 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4854  Z= 0.123
  Angle     :  0.607  10.383   6602  Z= 0.301
  Chirality :  0.040   0.124    755
  Planarity :  0.004   0.038    824
  Dihedral  :  3.898  17.629    667
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 28.88 %
    Favored  : 65.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.36), residues: 604
  helix:  1.46 (0.29), residues: 362
  sheet: -0.44 (0.72), residues: 52
  loop : -0.28 (0.50), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 273 
 TYR   0.019   0.001   TYR A 354 
 PHE   0.012   0.001   PHE A 351 
 TRP   0.008   0.001   TRP A 346 
 HIS   0.002   0.000   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4851)
  covalent geometry    : angle       0.60412 ( 6596)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       2.04583 (    6)
  hydrogen bonds       : bond        0.03876 (  289)
  hydrogen bonds       : angle       4.41073 (  849)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 84
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   80 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8262 (ttp80)
REVERT: B   90 ASP cc_start: 0.7728 (m-30) cc_final: 0.7319 (m-30)
  outliers start: 30
  outliers final: 25
  residues processed: 109
  average time/residue: 0.0584
  time to fit residues: 8.5150
Evaluate side-chains
  104 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLN
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  102 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0980
   chunk 17 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 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 = 0.4375 r_free = 0.4375 target = 0.206861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.171239 restraints weight = 6254.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 2.21
r_work: 0.3933 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3786 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4854  Z= 0.128
  Angle     :  0.613  10.880   6602  Z= 0.303
  Chirality :  0.040   0.190    755
  Planarity :  0.004   0.040    824
  Dihedral  :  3.896  17.684    667
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 29.47 %
    Favored  : 64.05 %
  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:  1.05 (0.36), residues: 604
  helix:  1.44 (0.28), residues: 363
  sheet: -0.50 (0.72), residues: 52
  loop : -0.30 (0.50), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 273 
 TYR   0.018   0.001   TYR A 354 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.007   0.001   TRP A 346 
 HIS   0.002   0.000   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4851)
  covalent geometry    : angle       0.61040 ( 6596)
  SS BOND              : bond        0.00395 (    3)
  SS BOND              : angle       1.79975 (    6)
  hydrogen bonds       : bond        0.03919 (  289)
  hydrogen bonds       : angle       4.39570 (  849)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   80 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8238 (ttp80)
REVERT: A  390 ASN cc_start: 0.8242 (m-40) cc_final: 0.7966 (m-40)
REVERT: B   90 ASP cc_start: 0.7718 (m-30) cc_final: 0.7288 (m-30)
  outliers start: 33
  outliers final: 29
  residues processed: 108
  average time/residue: 0.0567
  time to fit residues: 8.1862
Evaluate side-chains
  107 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 78
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLN
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   96 CYS
Chi-restraints excluded: chain B residue  102 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0040
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.4792

-------------------------------------------------------------------------------
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 = 0.4389 r_free = 0.4389 target = 0.208270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.172146 restraints weight = 6279.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.4047 rms_B_bonded: 2.28
r_work: 0.3933 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4854  Z= 0.121
  Angle     :  0.609  11.262   6602  Z= 0.300
  Chirality :  0.040   0.143    755
  Planarity :  0.004   0.042    824
  Dihedral  :  3.881  17.710    667
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 30.65 %
    Favored  : 63.65 %
  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 aren not related in a simple way.
  whole:  1.02 (0.36), residues: 604
  helix:  1.47 (0.28), residues: 363
  sheet: -1.21 (0.77), residues: 42
  loop : -0.27 (0.49), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 273 
 TYR   0.019   0.001   TYR A 354 
 PHE   0.012   0.001   PHE A 351 
 TRP   0.008   0.001   TRP A 346 
 HIS   0.001   0.000   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4851)
  covalent geometry    : angle       0.60731 ( 6596)
  SS BOND              : bond        0.00362 (    3)
  SS BOND              : angle       1.46303 (    6)
  hydrogen bonds       : bond        0.03839 (  289)
  hydrogen bonds       : angle       4.36354 (  849)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A   80 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7995 (ttp80)
REVERT: A  390 ASN cc_start: 0.8210 (m-40) cc_final: 0.7954 (m-40)
REVERT: B   90 ASP cc_start: 0.7469 (m-30) cc_final: 0.7108 (m-30)
  outliers start: 29
  outliers final: 26
  residues processed: 104
  average time/residue: 0.0542
  time to fit residues: 7.5144
Evaluate side-chains
  103 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLN
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  102 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0870
   chunk 59 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0070
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.4976

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 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 = 0.4389 r_free = 0.4389 target = 0.208214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.172602 restraints weight = 6133.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 2.23
r_work: 0.3917 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4854  Z= 0.123
  Angle     :  0.617  11.526   6602  Z= 0.302
  Chirality :  0.040   0.134    755
  Planarity :  0.004   0.036    824
  Dihedral  :  3.865  17.745    667
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 30.26 %
    Favored  : 63.85 %
  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:  1.03 (0.36), residues: 604
  helix:  1.48 (0.28), residues: 363
  sheet: -1.26 (0.76), residues: 42
  loop : -0.25 (0.49), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 273 
 TYR   0.018   0.001   TYR A 354 
 PHE   0.012   0.001   PHE A 351 
 TRP   0.008   0.001   TRP B  33 
 HIS   0.001   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4851)
  covalent geometry    : angle       0.61589 ( 6596)
  SS BOND              : bond        0.00438 (    3)
  SS BOND              : angle       1.55002 (    6)
  hydrogen bonds       : bond        0.03844 (  289)
  hydrogen bonds       : angle       4.33449 (  849)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 79
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A   80 ARG cc_start: 0.8287 (ttp80) cc_final: 0.8047 (ttp80)
REVERT: A  218 THR cc_start: 0.7788 (p) cc_final: 0.7544 (p)
REVERT: A  390 ASN cc_start: 0.8184 (m-40) cc_final: 0.7924 (m-40)
REVERT: A  485 MET cc_start: 0.7332 (ppp) cc_final: 0.7031 (ppp)
REVERT: B   90 ASP cc_start: 0.7410 (m-30) cc_final: 0.7018 (m-30)
  outliers start: 30
  outliers final: 27
  residues processed: 105
  average time/residue: 0.0565
  time to fit residues: 7.7551
Evaluate side-chains
  105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLN
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  102 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0020
   chunk 24 optimal weight:    0.0070
   chunk 11 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.3606

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 210 ASN ** 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 = 0.4401 r_free = 0.4401 target = 0.209374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.173502 restraints weight = 6205.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 2.26
r_work: 0.3947 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3799 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4854  Z= 0.117
  Angle     :  0.622  11.729   6602  Z= 0.303
  Chirality :  0.039   0.124    755
  Planarity :  0.004   0.038    824
  Dihedral  :  3.829  17.803    667
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 31.63 %
    Favored  : 63.65 %
  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 aren not related in a simple way.
  whole:  1.03 (0.36), residues: 604
  helix:  1.50 (0.28), residues: 363
  sheet: -1.26 (0.75), residues: 42
  loop : -0.28 (0.49), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 273 
 TYR   0.017   0.001   TYR A 354 
 PHE   0.012   0.001   PHE A 351 
 TRP   0.008   0.001   TRP B  33 
 HIS   0.001   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4851)
  covalent geometry    : angle       0.62074 ( 6596)
  SS BOND              : bond        0.00380 (    3)
  SS BOND              : angle       1.46205 (    6)
  hydrogen bonds       : bond        0.03728 (  289)
  hydrogen bonds       : angle       4.31385 (  849)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A    8 LYS cc_start: 0.8531 (mmtm) cc_final: 0.8249 (mptt)
REVERT: A   80 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8252 (ttp80)
REVERT: A  218 THR cc_start: 0.7978 (p) cc_final: 0.7742 (p)
REVERT: A  390 ASN cc_start: 0.8171 (m-40) cc_final: 0.7886 (m-40)
REVERT: B   90 ASP cc_start: 0.7536 (m-30) cc_final: 0.7122 (m-30)
  outliers start: 24
  outliers final: 22
  residues processed: 99
  average time/residue: 0.0564
  time to fit residues: 7.3838
Evaluate side-chains
  101 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLN
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  102 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   chunk 59 optimal weight:    0.1980
   chunk 47 optimal weight:    0.0980
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.209780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.174622 restraints weight = 6225.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.4059 rms_B_bonded: 2.18
r_work: 0.3964 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3815 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4854  Z= 0.122
  Angle     :  0.620  11.512   6602  Z= 0.303
  Chirality :  0.040   0.129    755
  Planarity :  0.004   0.038    824
  Dihedral  :  3.819  17.732    667
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 30.45 %
    Favored  : 64.05 %
  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:  1.05 (0.36), residues: 604
  helix:  1.51 (0.28), residues: 363
  sheet: -1.29 (0.75), residues: 42
  loop : -0.26 (0.49), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 273 
 TYR   0.018   0.001   TYR A 354 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A 109 
 HIS   0.002   0.000   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4851)
  covalent geometry    : angle       0.61917 ( 6596)
  SS BOND              : bond        0.00426 (    3)
  SS BOND              : angle       1.43582 (    6)
  hydrogen bonds       : bond        0.03778 (  289)
  hydrogen bonds       : angle       4.29906 (  849)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1211.17 seconds
wall clock time: 21 minutes 22.52 seconds (1282.52 seconds total)