Starting phenix.real_space_refine
on Fri Aug 22 16:49:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ug5_42214/08_2025/8ug5_42214.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ug5_42214/08_2025/8ug5_42214.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ug5_42214/08_2025/8ug5_42214.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ug5_42214/08_2025/8ug5_42214.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ug5_42214/08_2025/8ug5_42214.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ug5_42214/08_2025/8ug5_42214.cif"
  }
  resolution = 2.91
  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=   0.004
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      40      5.16       5
     C    4150      2.51       5
     N     978      2.21       5
     O     992      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  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: 6160
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3080
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 8, 'TRANS': 373}
          Chain breaks: 6
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.73, per 1000 atoms: 0.28
  Number of scatterers: 6160
  At special positions: 0
  Unit cell: (97.11, 87.15, 76.36, 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      40     16.00
     O     992      8.00
     N     978      7.00
     C    4150      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 183 " - pdb=" SG  CYS A 189 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 183 " - pdb=" SG  CYS B 189 " 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: 0.49
  Conformation dependent library (CDL) restraints added in 217.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1428

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 2 sheets defined
      82.7% alpha, 0.5% 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 53 through 56
    Processing helix  chain 'A' and resid 57 through 86
      removed outlier: 3.565A  pdb=" N   PHE A  63 " --> pdb=" O   ARG A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 119
    Processing helix  chain 'A' and resid 122 through 135
    Processing helix  chain 'A' and resid 158 through 185
    Processing helix  chain 'A' and resid 190 through 213
      removed outlier: 3.616A  pdb=" N   LYS A 196 " --> pdb=" O   VAL A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 244
      removed outlier: 3.550A  pdb=" N   PHE A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 340
    Processing helix  chain 'A' and resid 398 through 424
      removed outlier: 4.336A  pdb=" N   GLY A 403 " --> pdb=" O   GLN A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 435 through 464
      removed outlier: 3.924A  pdb=" N   ASP A 439 " --> pdb=" O   GLY A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 498
    Processing helix  chain 'A' and resid 504 through 511
    Processing helix  chain 'A' and resid 513 through 533
    Processing helix  chain 'A' and resid 551 through 579
      Proline residue:  A 559  - end of helix
      removed outlier: 3.907A  pdb=" N   VAL A 562 " --> pdb=" O   GLY A 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 56
    Processing helix  chain 'B' and resid 57 through 86
      removed outlier: 3.565A  pdb=" N   PHE B  63 " --> pdb=" O   ARG B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 119
    Processing helix  chain 'B' and resid 122 through 135
    Processing helix  chain 'B' and resid 158 through 185
    Processing helix  chain 'B' and resid 190 through 213
      removed outlier: 3.616A  pdb=" N   LYS B 196 " --> pdb=" O   VAL B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 244
      removed outlier: 3.550A  pdb=" N   PHE B 244 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 340
    Processing helix  chain 'B' and resid 398 through 424
      removed outlier: 4.337A  pdb=" N   GLY B 403 " --> pdb=" O   GLN B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 427
      No H-bonds generated for 'chain 'B' and resid 425 through 427'
    Processing helix  chain 'B' and resid 435 through 464
      removed outlier: 3.924A  pdb=" N   ASP B 439 " --> pdb=" O   GLY B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 498
    Processing helix  chain 'B' and resid 504 through 511
    Processing helix  chain 'B' and resid 513 through 533
    Processing helix  chain 'B' and resid 551 through 579
      Proline residue:  B 559  - end of helix
      removed outlier: 3.907A  pdb=" N   VAL B 562 " --> pdb=" O   GLY B 558 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 429
    Processing sheet with id=AA2, first strand: chain 'B' and resid 428 through 429

    502 hydrogen bonds defined for protein.
    1494 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: 0.95

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 973
        1.32 -     1.44: 1801
        1.44 -     1.57: 3486
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 6320
  Sorted by residual:
  bond pdb=" CA  SER A  86 "
       pdb=" CB  SER A  86 "
    ideal  model  delta    sigma   weight residual
    1.528  1.470  0.057 1.40e-02 5.10e+03 1.68e+01
  bond pdb=" CA  SER B  86 "
       pdb=" CB  SER B  86 "
    ideal  model  delta    sigma   weight residual
    1.528  1.470  0.057 1.40e-02 5.10e+03 1.67e+01
  bond pdb=" N   LYS A 511 "
       pdb=" CA  LYS A 511 "
    ideal  model  delta    sigma   weight residual
    1.460  1.488 -0.028 7.10e-03 1.98e+04 1.53e+01
  bond pdb=" N   LYS B 511 "
       pdb=" CA  LYS B 511 "
    ideal  model  delta    sigma   weight residual
    1.460  1.487 -0.027 7.10e-03 1.98e+04 1.45e+01
  bond pdb=" CA  SER A 221 "
       pdb=" CB  SER A 221 "
    ideal  model  delta    sigma   weight residual
    1.535  1.478  0.056 1.58e-02 4.01e+03 1.28e+01
  ... (remaining 6315 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 7430
        1.61 -     3.22: 899
        3.22 -     4.83: 195
        4.83 -     6.45: 30
        6.45 -     8.06: 10
  Bond angle restraints: 8564
  Sorted by residual:
  angle pdb=" N   VAL B  85 "
        pdb=" CA  VAL B  85 "
        pdb=" C   VAL B  85 "
      ideal   model   delta    sigma   weight residual
     113.10  106.94    6.16 9.70e-01 1.06e+00 4.04e+01
  angle pdb=" N   VAL A  85 "
        pdb=" CA  VAL A  85 "
        pdb=" C   VAL A  85 "
      ideal   model   delta    sigma   weight residual
     113.10  106.95    6.15 9.70e-01 1.06e+00 4.02e+01
  angle pdb=" N   ILE A 129 "
        pdb=" CA  ILE A 129 "
        pdb=" C   ILE A 129 "
      ideal   model   delta    sigma   weight residual
     110.42  104.54    5.88 9.60e-01 1.09e+00 3.76e+01
  angle pdb=" N   ILE B 129 "
        pdb=" CA  ILE B 129 "
        pdb=" C   ILE B 129 "
      ideal   model   delta    sigma   weight residual
     110.42  104.54    5.88 9.60e-01 1.09e+00 3.75e+01
  angle pdb=" N   ASN A 551 "
        pdb=" CA  ASN A 551 "
        pdb=" C   ASN A 551 "
      ideal   model   delta    sigma   weight residual
     114.39  106.33    8.06 1.45e+00 4.76e-01 3.09e+01
  ... (remaining 8559 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.14: 3162
       14.14 -    28.27: 306
       28.27 -    42.41: 100
       42.41 -    56.54: 26
       56.54 -    70.68: 10
  Dihedral angle restraints: 3604
    sinusoidal: 1386
      harmonic: 2218
  Sorted by residual:
  dihedral pdb=" CD  ARG A 133 "
           pdb=" NE  ARG A 133 "
           pdb=" CZ  ARG A 133 "
           pdb=" NH1 ARG A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   60.43  -60.43     1      1.00e+01 1.00e-02 4.86e+01
  dihedral pdb=" CD  ARG B 133 "
           pdb=" NE  ARG B 133 "
           pdb=" CZ  ARG B 133 "
           pdb=" NH1 ARG B 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   60.43  -60.43     1      1.00e+01 1.00e-02 4.86e+01
  dihedral pdb=" CD  ARG B  59 "
           pdb=" NE  ARG B  59 "
           pdb=" CZ  ARG B  59 "
           pdb=" NH1 ARG B  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   39.61  -39.61     1      1.00e+01 1.00e-02 2.20e+01
  ... (remaining 3601 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 718
       0.061 -    0.121: 160
       0.121 -    0.182: 83
       0.182 -    0.242: 27
       0.242 -    0.303: 12
  Chirality restraints: 1000
  Sorted by residual:
  chirality pdb=" CA  ILE A 129 "
            pdb=" N   ILE A 129 "
            pdb=" C   ILE A 129 "
            pdb=" CB  ILE A 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  ILE B 129 "
            pdb=" N   ILE B 129 "
            pdb=" C   ILE B 129 "
            pdb=" CB  ILE B 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  GLU A 185 "
            pdb=" N   GLU A 185 "
            pdb=" C   GLU A 185 "
            pdb=" CB  GLU A 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.94e+00
  ... (remaining 997 not shown)

  Planarity restraints: 1012
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 133 "   -0.956 9.50e-02 1.11e+02   4.29e-01 1.11e+02
        pdb=" NE  ARG A 133 "    0.057 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 133 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 133 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 133 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 133 "    0.956 9.50e-02 1.11e+02   4.28e-01 1.11e+02
        pdb=" NE  ARG B 133 "   -0.057 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 133 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 133 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 133 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  59 "   -0.692 9.50e-02 1.11e+02   3.10e-01 5.86e+01
        pdb=" NE  ARG A  59 "    0.041 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  59 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  59 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  59 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1009 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 2177
        2.85 -     3.36: 6308
        3.36 -     3.87: 10853
        3.87 -     4.39: 12068
        4.39 -     4.90: 20265
  Nonbonded interactions: 51671
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  99 "
            pdb=" OG  SER B 103 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   ILE A  99 "
            pdb=" OG  SER A 103 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" NE2 GLN A 486 "
            pdb=" OE1 GLN A 490 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" NE2 GLN B 486 "
            pdb=" OE1 GLN B 490 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" O   LEU A 407 "
            pdb=" OG  SER A 411 "
     model   vdw
     2.409 3.040
  ... (remaining 51666 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:             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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.550
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
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      :  0.008   0.071   6322  Z= 0.552
  Angle     :  1.134   8.056   8568  Z= 0.834
  Chirality :  0.075   0.303   1000
  Planarity :  0.024   0.429   1012
  Dihedral  : 13.475  70.676   2170
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  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:  0.42 (0.31), residues: 736
  helix:  0.90 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.28 (0.52), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 243 
 TYR   0.020   0.002   TYR B 101 
 PHE   0.010   0.002   PHE A 335 
 TRP   0.007   0.001   TRP A  54 
 HIS   0.009   0.001   HIS B 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00784 ( 6320)
  covalent geometry    : angle       1.13189 ( 8564)
  SS BOND              : bond        0.00195 (    2)
  SS BOND              : angle       3.60811 (    4)
  hydrogen bonds       : bond        0.14675 (  502)
  hydrogen bonds       : angle       6.34650 ( 1494)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6445 (ptp-170) cc_final: 0.5952 (ptp-170)
REVERT: A  147 MET cc_start: 0.5972 (mmm) cc_final: 0.5425 (mmp)
REVERT: A  506 TYR cc_start: 0.6069 (t80) cc_final: 0.5864 (t80)
REVERT: A  514 LYS cc_start: 0.6884 (tttt) cc_final: 0.6416 (ttpp)
REVERT: B  147 MET cc_start: 0.5940 (mmm) cc_final: 0.5448 (mmp)
REVERT: B  506 TYR cc_start: 0.6040 (t80) cc_final: 0.5773 (t80)
  outliers start: 0
  outliers final: 2
  residues processed: 174
  average time/residue: 0.4717
  time to fit residues: 86.1631
Evaluate side-chains
  95 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 93
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  445 ILE
Chi-restraints excluded: chain B residue  445 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 126 ASN
A 531 HIS
B  62 ASN
B 126 ASN
B 531 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.136220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.106204 restraints weight = 9082.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.02
r_work: 0.3205 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6322  Z= 0.134
  Angle     :  0.575   8.029   8568  Z= 0.296
  Chirality :  0.039   0.211   1000
  Planarity :  0.005   0.051   1012
  Dihedral  :  3.942  20.777    824
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.91 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.31), residues: 736
  helix:  1.78 (0.21), residues: 602
  sheet:  None (None), residues: 0
  loop : -1.42 (0.57), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  59 
 TYR   0.020   0.002   TYR A 510 
 PHE   0.016   0.001   PHE A 181 
 TRP   0.007   0.001   TRP A 144 
 HIS   0.006   0.001   HIS B 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6320)
  covalent geometry    : angle       0.57473 ( 8564)
  SS BOND              : bond        0.00183 (    2)
  SS BOND              : angle       0.57265 (    4)
  hydrogen bonds       : bond        0.04586 (  502)
  hydrogen bonds       : angle       4.12669 ( 1494)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6622 (ptp-170) cc_final: 0.6219 (ptp-170)
REVERT: A   52 ARG cc_start: 0.7930 (ptp90) cc_final: 0.7613 (ptp-170)
REVERT: A  110 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8496 (tm)
REVERT: A  133 ARG cc_start: 0.4379 (OUTLIER) cc_final: 0.3953 (mmm160)
REVERT: A  194 ILE cc_start: 0.8445 (mp) cc_final: 0.8209 (mp)
REVERT: A  334 MET cc_start: 0.8862 (mmt) cc_final: 0.8475 (mmp)
REVERT: A  514 LYS cc_start: 0.7042 (tttt) cc_final: 0.6728 (tppp)
REVERT: B   52 ARG cc_start: 0.7921 (ptp90) cc_final: 0.7642 (ptp-170)
REVERT: B   59 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6847 (ptm-80)
REVERT: B  110 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8512 (tm)
REVERT: B  133 ARG cc_start: 0.4305 (OUTLIER) cc_final: 0.3885 (mmm160)
REVERT: B  179 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6708 (mp0)
REVERT: B  334 MET cc_start: 0.8841 (mmt) cc_final: 0.8478 (mmp)
  outliers start: 20
  outliers final: 0
  residues processed: 110
  average time/residue: 0.3772
  time to fit residues: 44.1503
Evaluate side-chains
  97 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain B residue   59 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  133 ARG
Chi-restraints excluded: chain B residue  179 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   chunk 42 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0470
   chunk 74 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 72 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   overall best weight:    1.1480

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 151 HIS
B  62 ASN
B 151 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.135634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.104872 restraints weight = 9203.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.04
r_work: 0.3176 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6322  Z= 0.129
  Angle     :  0.508   7.214   8568  Z= 0.263
  Chirality :  0.037   0.127   1000
  Planarity :  0.003   0.032   1012
  Dihedral  :  3.510  16.448    820
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 15.91 %
    Favored  : 79.09 %
  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:  2.31 (0.30), residues: 736
  helix:  2.06 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -1.02 (0.58), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  52 
 TYR   0.019   0.001   TYR B 101 
 PHE   0.008   0.001   PHE A 335 
 TRP   0.004   0.001   TRP B 576 
 HIS   0.005   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6320)
  covalent geometry    : angle       0.50765 ( 8564)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       0.34800 (    4)
  hydrogen bonds       : bond        0.04136 (  502)
  hydrogen bonds       : angle       3.78899 ( 1494)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 95
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6574 (ptp-170) cc_final: 0.6186 (ptp-170)
REVERT: A  110 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8521 (tm)
REVERT: A  194 ILE cc_start: 0.8431 (mp) cc_final: 0.8039 (mp)
REVERT: A  217 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6345 (mm)
REVERT: A  334 MET cc_start: 0.8879 (mmt) cc_final: 0.8411 (mmp)
REVERT: A  514 LYS cc_start: 0.7197 (tttt) cc_final: 0.6842 (ttpp)
REVERT: B   52 ARG cc_start: 0.7959 (ptp90) cc_final: 0.7688 (ptp-170)
REVERT: B  110 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8518 (tm)
REVERT: B  127 GLN cc_start: 0.5939 (OUTLIER) cc_final: 0.5477 (mt0)
REVERT: B  128 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6914 (tt)
REVERT: B  194 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7987 (mp)
REVERT: B  217 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6355 (mm)
REVERT: B  334 MET cc_start: 0.8870 (mmt) cc_final: 0.8435 (mmp)
  outliers start: 33
  outliers final: 6
  residues processed: 110
  average time/residue: 0.3853
  time to fit residues: 45.1802
Evaluate side-chains
  98 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  406 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0970
   chunk 29 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 151 HIS
B  62 ASN
B 151 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.135164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.104433 restraints weight = 9184.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.03
r_work: 0.3163 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6322  Z= 0.150
  Angle     :  0.502   5.712   8568  Z= 0.264
  Chirality :  0.037   0.109   1000
  Planarity :  0.003   0.033   1012
  Dihedral  :  3.522  15.152    820
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 16.21 %
    Favored  : 78.94 %
  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:  2.46 (0.31), residues: 736
  helix:  2.10 (0.20), residues: 606
  sheet:  None (None), residues: 0
  loop : -0.60 (0.62), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.020   0.001   TYR A 101 
 PHE   0.018   0.002   PHE A 181 
 TRP   0.006   0.001   TRP A  54 
 HIS   0.006   0.001   HIS A 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6320)
  covalent geometry    : angle       0.50200 ( 8564)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       0.47954 (    4)
  hydrogen bonds       : bond        0.04205 (  502)
  hydrogen bonds       : angle       3.73931 ( 1494)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 85
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6627 (ptp-170) cc_final: 0.6199 (ptp-170)
REVERT: A  110 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8494 (tm)
REVERT: A  194 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8093 (mp)
REVERT: A  334 MET cc_start: 0.8879 (mmt) cc_final: 0.8462 (mmp)
REVERT: A  463 THR cc_start: 0.7637 (t) cc_final: 0.7424 (t)
REVERT: A  514 LYS cc_start: 0.7141 (tttt) cc_final: 0.6756 (ttpp)
REVERT: B   52 ARG cc_start: 0.8003 (ptp90) cc_final: 0.7741 (ptp-170)
REVERT: B   59 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7218 (ptm-80)
REVERT: B  110 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8470 (tm)
REVERT: B  127 GLN cc_start: 0.6007 (mp10) cc_final: 0.5579 (mt0)
REVERT: B  179 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6713 (mp0)
REVERT: B  194 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8024 (mp)
REVERT: B  334 MET cc_start: 0.8861 (mmt) cc_final: 0.8457 (mmp)
REVERT: B  463 THR cc_start: 0.7613 (t) cc_final: 0.7412 (t)
  outliers start: 32
  outliers final: 7
  residues processed: 106
  average time/residue: 0.3988
  time to fit residues: 44.9960
Evaluate side-chains
  94 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain B residue   59 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  406 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 127 GLN
A 151 HIS
B  62 ASN
B 151 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.135938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.105351 restraints weight = 9296.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.04
r_work: 0.3181 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6322  Z= 0.120
  Angle     :  0.479   6.819   8568  Z= 0.249
  Chirality :  0.036   0.128   1000
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.413  14.895    820
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 16.36 %
    Favored  : 79.09 %
  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:  2.55 (0.30), residues: 736
  helix:  2.21 (0.20), residues: 608
  sheet:  None (None), residues: 0
  loop : -0.94 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  52 
 TYR   0.017   0.001   TYR A 101 
 PHE   0.008   0.001   PHE A 461 
 TRP   0.006   0.001   TRP B 239 
 HIS   0.005   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6320)
  covalent geometry    : angle       0.47894 ( 8564)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       0.43636 (    4)
  hydrogen bonds       : bond        0.03899 (  502)
  hydrogen bonds       : angle       3.60724 ( 1494)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 85
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6606 (ptp-170) cc_final: 0.6204 (ptp-170)
REVERT: A  110 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8522 (tm)
REVERT: A  127 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.5867 (mt0)
REVERT: A  128 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6844 (tt)
REVERT: A  179 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6727 (mp0)
REVERT: A  194 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8114 (mp)
REVERT: A  334 MET cc_start: 0.8864 (mmt) cc_final: 0.8446 (mmp)
REVERT: A  463 THR cc_start: 0.7645 (t) cc_final: 0.7428 (t)
REVERT: A  508 MET cc_start: 0.6971 (mtp) cc_final: 0.6696 (mtt)
REVERT: A  514 LYS cc_start: 0.7212 (tttt) cc_final: 0.6866 (ttpp)
REVERT: B   59 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7204 (ptm-80)
REVERT: B  110 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8490 (tm)
REVERT: B  127 GLN cc_start: 0.6044 (mp10) cc_final: 0.5623 (mt0)
REVERT: B  128 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6912 (tt)
REVERT: B  179 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6645 (mp0)
REVERT: B  194 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7992 (mp)
REVERT: B  334 MET cc_start: 0.8858 (mmt) cc_final: 0.8451 (mmp)
REVERT: B  462 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7868 (mm)
REVERT: B  463 THR cc_start: 0.7647 (t) cc_final: 0.7426 (t)
REVERT: B  508 MET cc_start: 0.6994 (mtp) cc_final: 0.6724 (mtt)
  outliers start: 30
  outliers final: 8
  residues processed: 105
  average time/residue: 0.4314
  time to fit residues: 47.9746
Evaluate side-chains
  103 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  127 GLN
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain B residue   59 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  144 TRP
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  462 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 7 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 151 HIS
A 207 GLN
A 237 ASN
A 428 GLN
B  62 ASN
B 151 HIS
B 207 GLN
B 237 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.135822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.105595 restraints weight = 9234.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.02
r_work: 0.3182 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6322  Z= 0.117
  Angle     :  0.465   5.914   8568  Z= 0.244
  Chirality :  0.036   0.121   1000
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.351  13.960    820
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 16.21 %
    Favored  : 78.48 %
  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:  2.64 (0.30), residues: 736
  helix:  2.27 (0.20), residues: 608
  sheet:  None (None), residues: 0
  loop : -0.89 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  52 
 TYR   0.018   0.001   TYR A 101 
 PHE   0.014   0.001   PHE B 181 
 TRP   0.005   0.001   TRP B 239 
 HIS   0.005   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6320)
  covalent geometry    : angle       0.46509 ( 8564)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       0.38081 (    4)
  hydrogen bonds       : bond        0.03859 (  502)
  hydrogen bonds       : angle       3.58724 ( 1494)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 82
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6602 (ptp-170) cc_final: 0.6255 (ptp-170)
REVERT: A  104 MET cc_start: 0.8599 (mmm) cc_final: 0.8330 (mtp)
REVERT: A  110 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8524 (tm)
REVERT: A  127 GLN cc_start: 0.6158 (OUTLIER) cc_final: 0.5924 (mt0)
REVERT: A  179 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6712 (mp0)
REVERT: A  194 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8113 (mp)
REVERT: A  334 MET cc_start: 0.8890 (mmt) cc_final: 0.8380 (mmp)
REVERT: A  462 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7897 (mm)
REVERT: A  463 THR cc_start: 0.7652 (t) cc_final: 0.7429 (t)
REVERT: A  514 LYS cc_start: 0.7240 (tttt) cc_final: 0.6881 (ttpp)
REVERT: B   59 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7256 (ptm-80)
REVERT: B   62 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7470 (t0)
REVERT: B  104 MET cc_start: 0.8602 (mmm) cc_final: 0.8212 (mtp)
REVERT: B  110 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8498 (tm)
REVERT: B  127 GLN cc_start: 0.6025 (OUTLIER) cc_final: 0.5534 (mt0)
REVERT: B  128 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6901 (tt)
REVERT: B  179 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6641 (mp0)
REVERT: B  194 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8114 (mp)
REVERT: B  334 MET cc_start: 0.8890 (mmt) cc_final: 0.8391 (mmp)
REVERT: B  462 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7853 (mm)
REVERT: B  463 THR cc_start: 0.7665 (t) cc_final: 0.7448 (t)
REVERT: B  508 MET cc_start: 0.6954 (mtp) cc_final: 0.6725 (mtt)
  outliers start: 35
  outliers final: 8
  residues processed: 101
  average time/residue: 0.3774
  time to fit residues: 40.8218
Evaluate side-chains
  100 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  127 GLN
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain B residue   59 ARG
Chi-restraints excluded: chain B residue   62 ASN
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  144 TRP
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  462 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   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  62 ASN
A 127 GLN
A 151 HIS
A 207 GLN
B  62 ASN
B 207 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.135990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.105796 restraints weight = 9231.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.01
r_work: 0.3183 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6322  Z= 0.123
  Angle     :  0.466   5.533   8568  Z= 0.246
  Chirality :  0.036   0.114   1000
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.347  14.329    820
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 15.15 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.68 (0.30), residues: 736
  helix:  2.30 (0.20), residues: 608
  sheet:  None (None), residues: 0
  loop : -0.88 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 430 
 TYR   0.018   0.001   TYR A 101 
 PHE   0.016   0.001   PHE A 181 
 TRP   0.005   0.001   TRP B 239 
 HIS   0.005   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6320)
  covalent geometry    : angle       0.46601 ( 8564)
  SS BOND              : bond        0.00175 (    2)
  SS BOND              : angle       0.57059 (    4)
  hydrogen bonds       : bond        0.03858 (  502)
  hydrogen bonds       : angle       3.57990 ( 1494)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 83
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6562 (ptp-170) cc_final: 0.6227 (ptp-170)
REVERT: A   62 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7461 (t0)
REVERT: A  104 MET cc_start: 0.8570 (mmm) cc_final: 0.8368 (mtp)
REVERT: A  110 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8536 (tm)
REVERT: A  127 GLN cc_start: 0.6178 (OUTLIER) cc_final: 0.5965 (mt0)
REVERT: A  179 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6676 (mp0)
REVERT: A  334 MET cc_start: 0.8885 (mmt) cc_final: 0.8449 (mmp)
REVERT: A  462 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7908 (mm)
REVERT: A  463 THR cc_start: 0.7667 (t) cc_final: 0.7438 (t)
REVERT: A  508 MET cc_start: 0.7032 (mtp) cc_final: 0.6781 (mtt)
REVERT: A  514 LYS cc_start: 0.7174 (tttt) cc_final: 0.6806 (ttpp)
REVERT: B   59 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7231 (ptm-80)
REVERT: B   62 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7478 (t0)
REVERT: B  110 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8521 (tm)
REVERT: B  127 GLN cc_start: 0.6002 (OUTLIER) cc_final: 0.5495 (mt0)
REVERT: B  128 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6894 (tt)
REVERT: B  179 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6649 (mp0)
REVERT: B  194 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8122 (mp)
REVERT: B  462 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7934 (mm)
REVERT: B  463 THR cc_start: 0.7657 (t) cc_final: 0.7425 (t)
  outliers start: 37
  outliers final: 8
  residues processed: 106
  average time/residue: 0.3865
  time to fit residues: 43.4132
Evaluate side-chains
  102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  127 GLN
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain B residue   59 ARG
Chi-restraints excluded: chain B residue   62 ASN
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  144 TRP
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  462 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    0.2980
   chunk 72 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 127 GLN
A 207 GLN
B  62 ASN
B 151 HIS
B 207 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.135510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.105146 restraints weight = 9302.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.04
r_work: 0.3176 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6322  Z= 0.138
  Angle     :  0.481   5.374   8568  Z= 0.255
  Chirality :  0.037   0.112   1000
  Planarity :  0.003   0.035   1012
  Dihedral  :  3.388  13.627    820
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 16.82 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.62 (0.30), residues: 736
  helix:  2.26 (0.20), residues: 608
  sheet:  None (None), residues: 0
  loop : -0.89 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 430 
 TYR   0.019   0.001   TYR A 101 
 PHE   0.009   0.001   PHE A 335 
 TRP   0.006   0.001   TRP B 239 
 HIS   0.005   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6320)
  covalent geometry    : angle       0.48110 ( 8564)
  SS BOND              : bond        0.00324 (    2)
  SS BOND              : angle       0.56094 (    4)
  hydrogen bonds       : bond        0.03941 (  502)
  hydrogen bonds       : angle       3.60087 ( 1494)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6599 (ptp-170) cc_final: 0.6263 (ptp-170)
REVERT: A   62 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7458 (t0)
REVERT: A  110 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8562 (tm)
REVERT: A  179 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.6729 (mp0)
REVERT: A  462 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7933 (mm)
REVERT: A  463 THR cc_start: 0.7681 (t) cc_final: 0.7464 (t)
REVERT: A  508 MET cc_start: 0.7019 (mtp) cc_final: 0.6758 (mtt)
REVERT: A  514 LYS cc_start: 0.7151 (tttt) cc_final: 0.6777 (ttpp)
REVERT: B   59 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7216 (ptm-80)
REVERT: B   62 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7470 (t0)
REVERT: B  110 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8531 (tm)
REVERT: B  127 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5510 (mt0)
REVERT: B  128 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6901 (tt)
REVERT: B  179 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6637 (mp0)
REVERT: B  194 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8105 (mp)
REVERT: B  462 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7924 (mm)
REVERT: B  463 THR cc_start: 0.7666 (t) cc_final: 0.7436 (t)
REVERT: B  508 MET cc_start: 0.7043 (mtp) cc_final: 0.6787 (mtt)
  outliers start: 26
  outliers final: 8
  residues processed: 96
  average time/residue: 0.3970
  time to fit residues: 40.4196
Evaluate side-chains
  99 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain B residue   59 ARG
Chi-restraints excluded: chain B residue   62 ASN
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  144 TRP
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  462 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 48 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 207 GLN
B  62 ASN
B 207 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.136098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.105833 restraints weight = 9342.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.04
r_work: 0.3186 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6322  Z= 0.117
  Angle     :  0.469   5.347   8568  Z= 0.249
  Chirality :  0.036   0.113   1000
  Planarity :  0.003   0.035   1012
  Dihedral  :  3.330  13.844    820
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 17.12 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.71 (0.30), residues: 736
  helix:  2.32 (0.20), residues: 608
  sheet:  None (None), residues: 0
  loop : -0.88 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  66 
 TYR   0.017   0.001   TYR B 101 
 PHE   0.011   0.001   PHE A  63 
 TRP   0.006   0.001   TRP A 239 
 HIS   0.005   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6320)
  covalent geometry    : angle       0.46892 ( 8564)
  SS BOND              : bond        0.00320 (    2)
  SS BOND              : angle       0.57422 (    4)
  hydrogen bonds       : bond        0.03810 (  502)
  hydrogen bonds       : angle       3.56607 ( 1494)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6590 (ptp-170) cc_final: 0.6257 (ptp-170)
REVERT: A   62 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7429 (t0)
REVERT: A  110 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8556 (tm)
REVERT: A  127 GLN cc_start: 0.6452 (mt0) cc_final: 0.6231 (mt0)
REVERT: A  179 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.6745 (mp0)
REVERT: A  334 MET cc_start: 0.8873 (mmt) cc_final: 0.8447 (mmp)
REVERT: A  423 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7400 (mmm-85)
REVERT: A  462 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7916 (mm)
REVERT: A  463 THR cc_start: 0.7671 (t) cc_final: 0.7445 (t)
REVERT: A  508 MET cc_start: 0.7040 (mtp) cc_final: 0.6782 (mtt)
REVERT: A  514 LYS cc_start: 0.7169 (tttt) cc_final: 0.6589 (ttpp)
REVERT: B   59 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7217 (ptm-80)
REVERT: B   62 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7457 (t0)
REVERT: B  104 MET cc_start: 0.8613 (mmm) cc_final: 0.8015 (mtp)
REVERT: B  110 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8540 (tm)
REVERT: B  127 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5504 (mt0)
REVERT: B  128 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6874 (tt)
REVERT: B  179 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6643 (mp0)
REVERT: B  191 LYS cc_start: 0.6704 (OUTLIER) cc_final: 0.6095 (mttm)
REVERT: B  194 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8107 (mp)
REVERT: B  334 MET cc_start: 0.8878 (mmt) cc_final: 0.8453 (mmp)
REVERT: B  462 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7906 (mm)
REVERT: B  463 THR cc_start: 0.7643 (t) cc_final: 0.7423 (t)
REVERT: B  508 MET cc_start: 0.7031 (mtp) cc_final: 0.6788 (mtt)
  outliers start: 24
  outliers final: 6
  residues processed: 101
  average time/residue: 0.4098
  time to fit residues: 43.9527
Evaluate side-chains
  102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain B residue   59 ARG
Chi-restraints excluded: chain B residue   62 ASN
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  144 TRP
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  462 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0570
   chunk 65 optimal weight:    0.9980
   chunk 35 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 207 GLN
B  62 ASN
B 151 HIS
B 207 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.136686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.106240 restraints weight = 9420.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 2.06
r_work: 0.3188 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6322  Z= 0.116
  Angle     :  0.472   5.353   8568  Z= 0.251
  Chirality :  0.036   0.127   1000
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.292  13.117    820
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.88 %
    Favored  : 78.79 %
  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:  2.78 (0.30), residues: 736
  helix:  2.37 (0.20), residues: 608
  sheet:  None (None), residues: 0
  loop : -0.83 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  52 
 TYR   0.017   0.001   TYR A 101 
 PHE   0.017   0.001   PHE A 181 
 TRP   0.006   0.001   TRP B 239 
 HIS   0.005   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6320)
  covalent geometry    : angle       0.47229 ( 8564)
  SS BOND              : bond        0.00288 (    2)
  SS BOND              : angle       0.72888 (    4)
  hydrogen bonds       : bond        0.03759 (  502)
  hydrogen bonds       : angle       3.55583 ( 1494)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6622 (ptp-170) cc_final: 0.6300 (ptp-170)
REVERT: A   62 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7487 (t0)
REVERT: A  104 MET cc_start: 0.8615 (mmm) cc_final: 0.7971 (mtp)
REVERT: A  110 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8558 (tm)
REVERT: A  127 GLN cc_start: 0.6464 (mt0) cc_final: 0.6251 (mt0)
REVERT: A  179 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.6742 (mp0)
REVERT: A  334 MET cc_start: 0.8881 (mmt) cc_final: 0.8435 (mmp)
REVERT: A  423 ARG cc_start: 0.7769 (mmm160) cc_final: 0.7422 (mmm-85)
REVERT: A  462 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7891 (mm)
REVERT: A  463 THR cc_start: 0.7689 (t) cc_final: 0.7472 (t)
REVERT: A  508 MET cc_start: 0.7046 (mtp) cc_final: 0.6787 (mtt)
REVERT: A  514 LYS cc_start: 0.7286 (tttt) cc_final: 0.6709 (ttpp)
REVERT: B   59 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7223 (ptm-80)
REVERT: B   62 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7468 (t0)
REVERT: B  104 MET cc_start: 0.8537 (mmm) cc_final: 0.7779 (mtp)
REVERT: B  110 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8527 (tm)
REVERT: B  127 GLN cc_start: 0.5956 (OUTLIER) cc_final: 0.5488 (mt0)
REVERT: B  128 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6878 (tt)
REVERT: B  179 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6668 (mp0)
REVERT: B  191 LYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6136 (mttm)
REVERT: B  334 MET cc_start: 0.8881 (mmt) cc_final: 0.8446 (mmp)
REVERT: B  462 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7894 (mm)
REVERT: B  463 THR cc_start: 0.7646 (t) cc_final: 0.7419 (t)
REVERT: B  508 MET cc_start: 0.7013 (mtp) cc_final: 0.6760 (mtt)
  outliers start: 22
  outliers final: 6
  residues processed: 99
  average time/residue: 0.4150
  time to fit residues: 43.5877
Evaluate side-chains
  100 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain B residue   59 ARG
Chi-restraints excluded: chain B residue   62 ASN
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  144 TRP
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  462 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 25 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 207 GLN
B  62 ASN
B 207 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.136644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.106509 restraints weight = 9275.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.05
r_work: 0.3191 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.3454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6322  Z= 0.120
  Angle     :  0.478   5.360   8568  Z= 0.255
  Chirality :  0.036   0.123   1000
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.260  13.411    820
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.58 %
    Favored  : 78.94 %
  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:  2.84 (0.30), residues: 736
  helix:  2.44 (0.19), residues: 606
  sheet:  None (None), residues: 0
  loop : -0.94 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  59 
 TYR   0.017   0.001   TYR A 101 
 PHE   0.008   0.001   PHE A  63 
 TRP   0.006   0.001   TRP B 239 
 HIS   0.005   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6320)
  covalent geometry    : angle       0.47754 ( 8564)
  SS BOND              : bond        0.00296 (    2)
  SS BOND              : angle       0.84464 (    4)
  hydrogen bonds       : bond        0.03771 (  502)
  hydrogen bonds       : angle       3.59500 ( 1494)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1893.45 seconds
wall clock time: 32 minutes 55.77 seconds (1975.77 seconds total)