Starting phenix.real_space_refine
on Sun Apr 27 15:48:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ug5_42214/04_2025/8ug5_42214.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ug5_42214/04_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_42214/04_2025/8ug5_42214.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ug5_42214/04_2025/8ug5_42214.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ug5_42214/04_2025/8ug5_42214.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ug5_42214/04_2025/8ug5_42214.cif"
  }
  resolution = 2.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.42, per 1000 atoms: 0.88
  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: 1.68
  Conformation dependent library (CDL) restraints added in 909.0 milliseconds
  

  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: 0.61
  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: 1.74

  Time building geometry restraints manager: 1.97 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: 0.03
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:             1.430
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.800
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  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:12.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.840
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.007   0.001   TRP A  54 
 HIS   0.009   0.001   HIS B 567 
 PHE   0.010   0.002   PHE A 335 
 TYR   0.020   0.002   TYR B 101 
 ARG   0.003   0.001   ARG A 243 

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

*********************** 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  : 0.720 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6445 (ptp-170) cc_final: 0.5950 (ptp-170)
REVERT: A  147 MET cc_start: 0.5972 (mmm) cc_final: 0.5424 (mmp)
REVERT: A  506 TYR cc_start: 0.6069 (t80) cc_final: 0.5838 (t80)
REVERT: A  514 LYS cc_start: 0.6884 (tttt) cc_final: 0.6413 (ttpp)
REVERT: B  147 MET cc_start: 0.5940 (mmm) cc_final: 0.5446 (mmp)
REVERT: B  506 TYR cc_start: 0.6040 (t80) cc_final: 0.5797 (t80)
  outliers start: 0
  outliers final: 2
  residues processed: 174
  average time/residue: 1.0567
  time to fit residues: 193.3568
Evaluate side-chains
  96 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
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 64 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3736 r_free = 0.3736 target = 0.135792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.105719 restraints weight = 9003.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.01
r_work: 0.3192 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.2466

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= 0.145
  Angle     :  0.573   8.235   8568  Z= 0.299
  Chirality :  0.039   0.197   1000
  Planarity :  0.005   0.058   1012
  Dihedral  :  3.938  21.496    824
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.06 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.31), residues: 736
  helix:  1.71 (0.20), residues: 602
  sheet:  None (None), residues: 0
  loop : -1.49 (0.57), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 144 
 HIS   0.006   0.001   HIS B 567 
 PHE   0.016   0.001   PHE A 181 
 TYR   0.019   0.002   TYR B 510 
 ARG   0.007   0.001   ARG A  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04660 (  502)
  hydrogen bonds       : angle       4.15861 ( 1494)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       0.59185 (    4)
  covalent geometry    : bond        0.00310 ( 6320)
  covalent geometry    : angle       0.57254 ( 8564)

*********************** 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
  125 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6612 (ptp-170) cc_final: 0.6245 (ptp-170)
REVERT: A   52 ARG cc_start: 0.7936 (ptp90) cc_final: 0.7585 (ptp-170)
REVERT: A  110 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8501 (tm)
REVERT: A  133 ARG cc_start: 0.4304 (OUTLIER) cc_final: 0.3935 (mmm160)
REVERT: A  334 MET cc_start: 0.8865 (mmt) cc_final: 0.8505 (mmp)
REVERT: A  514 LYS cc_start: 0.7090 (tttt) cc_final: 0.6522 (ttpp)
REVERT: B   52 ARG cc_start: 0.7922 (ptp90) cc_final: 0.7646 (ptp-170)
REVERT: B   59 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6879 (ptm-80)
REVERT: B  110 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8500 (tm)
REVERT: B  133 ARG cc_start: 0.4213 (OUTLIER) cc_final: 0.3829 (mmm160)
REVERT: B  179 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6715 (mp0)
REVERT: B  334 MET cc_start: 0.8837 (mmt) cc_final: 0.8523 (mmp)
  outliers start: 23
  outliers final: 2
  residues processed: 112
  average time/residue: 0.9020
  time to fit residues: 107.7001
Evaluate side-chains
  99 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain A residue  320 THR
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
Chi-restraints excluded: chain B residue  320 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 40 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0770
   chunk 69 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7340

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
B  62 ASN
B 126 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 = 0.3748 r_free = 0.3748 target = 0.136935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.106237 restraints weight = 9105.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.04
r_work: 0.3191 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6322  Z= 0.114
  Angle     :  0.498   6.984   8568  Z= 0.257
  Chirality :  0.036   0.120   1000
  Planarity :  0.003   0.042   1012
  Dihedral  :  3.452  16.138    820
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 15.76 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.31), residues: 736
  helix:  2.14 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.98 (0.59), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  94 
 HIS   0.005   0.001   HIS A 151 
 PHE   0.006   0.001   PHE A 530 
 TYR   0.019   0.001   TYR A 506 
 ARG   0.004   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03977 (  502)
  hydrogen bonds       : angle       3.71893 ( 1494)
  SS BOND              : bond        0.00192 (    2)
  SS BOND              : angle       0.40650 (    4)
  covalent geometry    : bond        0.00240 ( 6320)
  covalent geometry    : angle       0.49808 ( 8564)

*********************** 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
  131 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 100
  time to evaluate  : 0.679 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6548 (ptp-170) cc_final: 0.6152 (ptp-170)
REVERT: A  110 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8505 (tm)
REVERT: A  127 GLN cc_start: 0.5975 (mp10) cc_final: 0.5593 (mt0)
REVERT: A  144 TRP cc_start: 0.4764 (OUTLIER) cc_final: 0.2993 (t60)
REVERT: A  194 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7974 (mp)
REVERT: A  217 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6342 (mm)
REVERT: A  514 LYS cc_start: 0.7200 (tttt) cc_final: 0.6831 (ttpp)
REVERT: A  550 TYR cc_start: 0.3992 (p90) cc_final: 0.3755 (p90)
REVERT: B  104 MET cc_start: 0.8420 (mmm) cc_final: 0.8129 (mtp)
REVERT: B  110 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8485 (tm)
REVERT: B  127 GLN cc_start: 0.5845 (mp10) cc_final: 0.5411 (mt0)
REVERT: B  144 TRP cc_start: 0.4648 (OUTLIER) cc_final: 0.2948 (t60)
REVERT: B  194 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7987 (mp)
REVERT: B  217 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6335 (mm)
REVERT: B  334 MET cc_start: 0.8887 (mmt) cc_final: 0.8507 (mmp)
  outliers start: 31
  outliers final: 2
  residues processed: 113
  average time/residue: 0.8410
  time to fit residues: 101.4795
Evaluate side-chains
  100 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  144 TRP
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  217 ILE
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 35 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   overall best weight:    0.9982

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.136656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.106011 restraints weight = 9239.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.03
r_work: 0.3193 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3009

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     :  0.474   5.302   8568  Z= 0.247
  Chirality :  0.036   0.115   1000
  Planarity :  0.003   0.031   1012
  Dihedral  :  3.381  14.832    820
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 16.97 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.68 (0.30), residues: 736
  helix:  2.27 (0.20), residues: 606
  sheet:  None (None), residues: 0
  loop : -0.70 (0.61), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.005   0.001   HIS A 151 
 PHE   0.018   0.001   PHE A 181 
 TYR   0.019   0.001   TYR A 101 
 ARG   0.002   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03899 (  502)
  hydrogen bonds       : angle       3.61807 ( 1494)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       0.42124 (    4)
  covalent geometry    : bond        0.00256 ( 6320)
  covalent geometry    : angle       0.47369 ( 8564)

*********************** 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
  126 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 94
  time to evaluate  : 0.660 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6641 (ptp-170) cc_final: 0.6212 (ptp-170)
REVERT: A  110 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8499 (tm)
REVERT: A  127 GLN cc_start: 0.6027 (mp10) cc_final: 0.5646 (mt0)
REVERT: A  128 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6845 (tt)
REVERT: A  194 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8083 (mp)
REVERT: A  463 THR cc_start: 0.7627 (t) cc_final: 0.7404 (t)
REVERT: A  514 LYS cc_start: 0.7201 (tttt) cc_final: 0.6851 (ttpp)
REVERT: B   57 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6153 (tm-30)
REVERT: B   59 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7161 (ptm-80)
REVERT: B  110 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8502 (tm)
REVERT: B  127 GLN cc_start: 0.5947 (mp10) cc_final: 0.5563 (mt0)
REVERT: B  144 TRP cc_start: 0.4752 (OUTLIER) cc_final: 0.2965 (t60)
REVERT: B  179 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6656 (mp0)
REVERT: B  194 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8012 (mp)
REVERT: B  463 THR cc_start: 0.7599 (t) cc_final: 0.7390 (t)
  outliers start: 32
  outliers final: 6
  residues processed: 113
  average time/residue: 1.0098
  time to fit residues: 120.7848
Evaluate side-chains
  102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  128 LEU
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   57 GLU
Chi-restraints excluded: chain B residue   59 ARG
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  110 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  406 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 18 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 39 optimal weight:    0.7980
   chunk 71 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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
B  62 ASN
B 151 HIS
B 207 GLN
B 237 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.134828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.104785 restraints weight = 9236.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 1.99
r_work: 0.3170 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.3066

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= 0.148
  Angle     :  0.500   6.032   8568  Z= 0.263
  Chirality :  0.037   0.126   1000
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.413  15.027    820
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 15.76 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.30), residues: 736
  helix:  2.20 (0.20), residues: 606
  sheet:  None (None), residues: 0
  loop : -0.69 (0.61), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.006   0.001   HIS A 567 
 PHE   0.011   0.001   PHE A 335 
 TYR   0.020   0.001   TYR A 101 
 ARG   0.002   0.000   ARG B 425 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04109 (  502)
  hydrogen bonds       : angle       3.65751 ( 1494)
  SS BOND              : bond        0.00246 (    2)
  SS BOND              : angle       0.54623 (    4)
  covalent geometry    : bond        0.00341 ( 6320)
  covalent geometry    : angle       0.49968 ( 8564)

*********************** 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
  120 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 82
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6595 (ptp-170) cc_final: 0.6267 (ptp-170)
REVERT: A  110 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8506 (tm)
REVERT: A  127 GLN cc_start: 0.6068 (OUTLIER) cc_final: 0.5676 (mt0)
REVERT: A  128 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6838 (tt)
REVERT: A  179 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6700 (mp0)
REVERT: A  217 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6290 (mm)
REVERT: A  462 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7900 (mm)
REVERT: A  463 THR cc_start: 0.7667 (t) cc_final: 0.7437 (t)
REVERT: A  514 LYS cc_start: 0.7166 (tttt) cc_final: 0.6794 (ttpp)
REVERT: B   59 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7246 (ptm-80)
REVERT: B  110 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8488 (tm)
REVERT: B  127 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.5563 (mt0)
REVERT: B  179 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6622 (mp0)
REVERT: B  194 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8008 (mp)
REVERT: B  462 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7929 (mm)
REVERT: B  463 THR cc_start: 0.7638 (t) cc_final: 0.7416 (t)
  outliers start: 38
  outliers final: 10
  residues processed: 105
  average time/residue: 0.8767
  time to fit residues: 98.2258
Evaluate side-chains
  100 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
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  216 LYS
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   59 ARG
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  127 GLN
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  216 LYS
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 38 optimal weight:    0.0370
   chunk 35 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 39 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.9662

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.135687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.105771 restraints weight = 9190.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.99
r_work: 0.3183 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6322  Z= 0.116
  Angle     :  0.472   7.174   8568  Z= 0.247
  Chirality :  0.036   0.121   1000
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.313  13.863    820
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 16.67 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.30), residues: 736
  helix:  2.31 (0.20), residues: 608
  sheet:  None (None), residues: 0
  loop : -0.90 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.004   0.001   HIS A 151 
 PHE   0.017   0.001   PHE A 181 
 TYR   0.018   0.001   TYR B 101 
 ARG   0.002   0.000   ARG B 430 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  502)
  hydrogen bonds       : angle       3.57025 ( 1494)
  SS BOND              : bond        0.00250 (    2)
  SS BOND              : angle       0.51737 (    4)
  covalent geometry    : bond        0.00257 ( 6320)
  covalent geometry    : angle       0.47176 ( 8564)

*********************** 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
  116 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 85
  time to evaluate  : 0.661 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6616 (ptp-170) cc_final: 0.6277 (ptp-170)
REVERT: A   62 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7420 (t0)
REVERT: A  104 MET cc_start: 0.8531 (mmm) cc_final: 0.8314 (mtp)
REVERT: A  110 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8534 (tm)
REVERT: A  127 GLN cc_start: 0.5990 (OUTLIER) cc_final: 0.5523 (mt0)
REVERT: A  179 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6674 (mp0)
REVERT: A  216 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.6092 (mttt)
REVERT: A  334 MET cc_start: 0.8894 (mmt) cc_final: 0.8454 (mmp)
REVERT: A  462 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7877 (mm)
REVERT: A  463 THR cc_start: 0.7673 (t) cc_final: 0.7442 (t)
REVERT: A  508 MET cc_start: 0.7033 (mtp) cc_final: 0.6720 (mtt)
REVERT: A  514 LYS cc_start: 0.7237 (tttt) cc_final: 0.6878 (ttpp)
REVERT: B   59 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7213 (ptm-80)
REVERT: B   62 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7426 (t0)
REVERT: B  110 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8508 (tm)
REVERT: B  127 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5552 (mt0)
REVERT: B  144 TRP cc_start: 0.4870 (OUTLIER) cc_final: 0.2873 (t60)
REVERT: B  179 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6656 (mp0)
REVERT: B  194 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8132 (mp)
REVERT: B  216 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.6104 (mttt)
REVERT: B  423 ARG cc_start: 0.7686 (mmm160) cc_final: 0.7388 (mmm-85)
REVERT: B  462 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7856 (mm)
REVERT: B  463 THR cc_start: 0.7664 (t) cc_final: 0.7450 (t)
REVERT: B  508 MET cc_start: 0.6996 (mtp) cc_final: 0.6748 (mtt)
  outliers start: 31
  outliers final: 6
  residues processed: 104
  average time/residue: 0.9721
  time to fit residues: 107.2967
Evaluate side-chains
  104 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
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  216 LYS
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  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  216 LYS
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 61 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0570
   chunk 46 optimal weight:   20.0000
   chunk 50 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   overall best weight:    0.6902

-------------------------------------------------------------------------------
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
B  62 ASN
B 151 HIS
** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

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 = 0.136650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.106503 restraints weight = 9206.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.01
r_work: 0.3195 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6322  Z= 0.112
  Angle     :  0.464   6.561   8568  Z= 0.244
  Chirality :  0.036   0.118   1000
  Planarity :  0.003   0.033   1012
  Dihedral  :  3.286  14.220    820
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 16.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.83 (0.30), residues: 736
  helix:  2.41 (0.20), residues: 608
  sheet:  None (None), residues: 0
  loop : -0.86 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.005   0.001   HIS A 151 
 PHE   0.007   0.001   PHE A 461 
 TYR   0.017   0.001   TYR B 101 
 ARG   0.005   0.000   ARG A  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03714 (  502)
  hydrogen bonds       : angle       3.50692 ( 1494)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       0.72266 (    4)
  covalent geometry    : bond        0.00246 ( 6320)
  covalent geometry    : angle       0.46421 ( 8564)

*********************** 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
  119 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 86
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6583 (ptp-170) cc_final: 0.6242 (ptp-170)
REVERT: A   62 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7460 (t0)
REVERT: A  110 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8528 (tm)
REVERT: A  127 GLN cc_start: 0.6011 (OUTLIER) cc_final: 0.5532 (mt0)
REVERT: A  179 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.6698 (mp0)
REVERT: A  216 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.6097 (mttt)
REVERT: A  334 MET cc_start: 0.8892 (mmt) cc_final: 0.8399 (mmp)
REVERT: A  423 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7387 (mmm-85)
REVERT: A  462 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7893 (mm)
REVERT: A  463 THR cc_start: 0.7649 (t) cc_final: 0.7424 (t)
REVERT: A  508 MET cc_start: 0.7018 (mtp) cc_final: 0.6688 (mtt)
REVERT: A  514 LYS cc_start: 0.7273 (tttt) cc_final: 0.6691 (ttpp)
REVERT: B   59 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7242 (ptm-80)
REVERT: B   62 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7450 (t0)
REVERT: B   95 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6907 (pt)
REVERT: B  110 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8519 (tm)
REVERT: B  127 GLN cc_start: 0.6002 (OUTLIER) cc_final: 0.5535 (mt0)
REVERT: B  179 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6621 (mp0)
REVERT: B  191 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6077 (mttm)
REVERT: B  194 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8115 (mp)
REVERT: B  216 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.6071 (mttt)
REVERT: B  462 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7873 (mm)
REVERT: B  463 THR cc_start: 0.7663 (t) cc_final: 0.7439 (t)
REVERT: B  508 MET cc_start: 0.6933 (mtp) cc_final: 0.6686 (mtt)
  outliers start: 33
  outliers final: 4
  residues processed: 106
  average time/residue: 0.9729
  time to fit residues: 109.2568
Evaluate side-chains
  102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
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  216 LYS
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   95 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  127 GLN
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  216 LYS
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 65 optimal weight:    0.9980
   chunk 41 optimal weight:    0.2980
   chunk 32 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 73 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   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 207 GLN
B  62 ASN
** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.136640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.107225 restraints weight = 9169.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.99
r_work: 0.3201 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.3373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6322  Z= 0.113
  Angle     :  0.470   6.205   8568  Z= 0.248
  Chirality :  0.036   0.115   1000
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.279  13.094    820
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 17.27 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.88 (0.30), residues: 736
  helix:  2.44 (0.20), residues: 608
  sheet:  None (None), residues: 0
  loop : -0.82 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.005   0.001   HIS B 151 
 PHE   0.007   0.001   PHE A 461 
 TYR   0.017   0.001   TYR B 101 
 ARG   0.005   0.000   ARG B 423 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03700 (  502)
  hydrogen bonds       : angle       3.46829 ( 1494)
  SS BOND              : bond        0.00315 (    2)
  SS BOND              : angle       0.60655 (    4)
  covalent geometry    : bond        0.00254 ( 6320)
  covalent geometry    : angle       0.46969 ( 8564)

*********************** 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
  110 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6572 (ptp-170) cc_final: 0.6243 (ptp-170)
REVERT: A   62 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7466 (t0)
REVERT: A  110 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8524 (tm)
REVERT: A  127 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5535 (mt0)
REVERT: A  179 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6715 (mp0)
REVERT: A  216 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.6072 (mttt)
REVERT: A  334 MET cc_start: 0.8894 (mmt) cc_final: 0.8383 (mmp)
REVERT: A  462 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7879 (mm)
REVERT: A  463 THR cc_start: 0.7645 (t) cc_final: 0.7425 (t)
REVERT: A  508 MET cc_start: 0.7008 (mtp) cc_final: 0.6703 (mtt)
REVERT: A  514 LYS cc_start: 0.7268 (tttt) cc_final: 0.6685 (ttpp)
REVERT: B   59 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7258 (ptm-80)
REVERT: B   62 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7512 (t0)
REVERT: B  110 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8526 (tm)
REVERT: B  127 GLN cc_start: 0.6020 (OUTLIER) cc_final: 0.5552 (mt0)
REVERT: B  179 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6651 (mp0)
REVERT: B  191 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6097 (mttm)
REVERT: B  216 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.6091 (mttt)
REVERT: B  462 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7867 (mm)
REVERT: B  463 THR cc_start: 0.7640 (t) cc_final: 0.7426 (t)
  outliers start: 26
  outliers final: 7
  residues processed: 101
  average time/residue: 1.0217
  time to fit residues: 109.3870
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  : 0.680 
-------------------------------------------------------------------------------
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  216 LYS
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  144 TRP
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  216 LYS
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 5 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.136490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.106901 restraints weight = 9277.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.00
r_work: 0.3193 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6322  Z= 0.117
  Angle     :  0.472   5.936   8568  Z= 0.250
  Chirality :  0.036   0.126   1000
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.242  13.711    820
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 17.58 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.89 (0.30), residues: 736
  helix:  2.48 (0.20), residues: 606
  sheet:  None (None), residues: 0
  loop : -0.93 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.005   0.001   HIS B 151 
 PHE   0.017   0.001   PHE A 181 
 TYR   0.018   0.001   TYR A 101 
 ARG   0.005   0.000   ARG A 423 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03702 (  502)
  hydrogen bonds       : angle       3.50259 ( 1494)
  SS BOND              : bond        0.00278 (    2)
  SS BOND              : angle       0.68240 (    4)
  covalent geometry    : bond        0.00269 ( 6320)
  covalent geometry    : angle       0.47154 ( 8564)

*********************** 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
  106 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6555 (ptp-170) cc_final: 0.6236 (ptp-170)
REVERT: A   62 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7451 (t0)
REVERT: A  104 MET cc_start: 0.8608 (mmm) cc_final: 0.8152 (mtp)
REVERT: A  110 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8551 (tm)
REVERT: A  127 GLN cc_start: 0.6010 (OUTLIER) cc_final: 0.5530 (mt0)
REVERT: A  179 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6715 (mp0)
REVERT: A  216 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.6143 (mttt)
REVERT: A  334 MET cc_start: 0.8899 (mmt) cc_final: 0.8395 (mmp)
REVERT: A  462 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7911 (mm)
REVERT: A  463 THR cc_start: 0.7677 (t) cc_final: 0.7464 (t)
REVERT: A  508 MET cc_start: 0.7062 (mtp) cc_final: 0.6789 (mtt)
REVERT: A  514 LYS cc_start: 0.7232 (tttt) cc_final: 0.6647 (ttpp)
REVERT: B   59 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7215 (ptm-80)
REVERT: B   62 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7467 (t0)
REVERT: B  110 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8514 (tm)
REVERT: B  127 GLN cc_start: 0.6018 (OUTLIER) cc_final: 0.5547 (mt0)
REVERT: B  144 TRP cc_start: 0.4932 (OUTLIER) cc_final: 0.3611 (p90)
REVERT: B  179 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6655 (mp0)
REVERT: B  191 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6017 (mttm)
REVERT: B  216 LYS cc_start: 0.6404 (OUTLIER) cc_final: 0.6087 (mttt)
REVERT: B  462 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7860 (mm)
REVERT: B  463 THR cc_start: 0.7645 (t) cc_final: 0.7425 (t)
REVERT: B  508 MET cc_start: 0.7065 (mtp) cc_final: 0.6800 (mtt)
  outliers start: 24
  outliers final: 6
  residues processed: 98
  average time/residue: 0.9497
  time to fit residues: 99.0857
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  : 0.741 
-------------------------------------------------------------------------------
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  216 LYS
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  144 TRP
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  216 LYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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
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 = 0.3732 r_free = 0.3732 target = 0.135939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.106251 restraints weight = 9339.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 1.99
r_work: 0.3184 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6322  Z= 0.131
  Angle     :  0.485   5.690   8568  Z= 0.258
  Chirality :  0.036   0.124   1000
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.271  13.810    820
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 16.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.30), residues: 736
  helix:  2.42 (0.20), residues: 606
  sheet:  None (None), residues: 0
  loop : -0.89 (0.58), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  94 
 HIS   0.005   0.001   HIS A 151 
 PHE   0.009   0.001   PHE A 461 
 TYR   0.019   0.001   TYR A 101 
 ARG   0.005   0.001   ARG A 423 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03795 (  502)
  hydrogen bonds       : angle       3.53001 ( 1494)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       0.91271 (    4)
  covalent geometry    : bond        0.00304 ( 6320)
  covalent geometry    : angle       0.48502 ( 8564)

********************** 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
  111 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 81
  time to evaluate  : 0.668 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6634 (ptp-170) cc_final: 0.6305 (ptp-170)
REVERT: A   62 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7405 (t0)
REVERT: A  104 MET cc_start: 0.8601 (mmm) cc_final: 0.8235 (mtp)
REVERT: A  110 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8551 (tm)
REVERT: A  127 GLN cc_start: 0.5966 (OUTLIER) cc_final: 0.5481 (mt0)
REVERT: A  179 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6704 (mp0)
REVERT: A  216 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.6145 (mttt)
REVERT: A  462 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7920 (mm)
REVERT: A  463 THR cc_start: 0.7693 (t) cc_final: 0.7472 (t)
REVERT: A  508 MET cc_start: 0.7072 (mtp) cc_final: 0.6794 (mtt)
REVERT: A  514 LYS cc_start: 0.7194 (tttt) cc_final: 0.6610 (ttpp)
REVERT: B   59 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7226 (ptm-80)
REVERT: B   62 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7483 (t0)
REVERT: B  104 MET cc_start: 0.8632 (mmm) cc_final: 0.8150 (mtp)
REVERT: B  110 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8537 (tm)
REVERT: B  127 GLN cc_start: 0.6010 (OUTLIER) cc_final: 0.5527 (mt0)
REVERT: B  144 TRP cc_start: 0.4956 (OUTLIER) cc_final: 0.3683 (p90)
REVERT: B  179 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6645 (mp0)
REVERT: B  191 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.6051 (mttm)
REVERT: B  216 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.6117 (mttt)
REVERT: B  462 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7878 (mm)
REVERT: B  463 THR cc_start: 0.7625 (t) cc_final: 0.7399 (t)
REVERT: B  508 MET cc_start: 0.7039 (mtp) cc_final: 0.6765 (mtt)
  outliers start: 30
  outliers final: 7
  residues processed: 101
  average time/residue: 0.9621
  time to fit residues: 103.5780
Evaluate side-chains
  104 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
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  216 LYS
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   95 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  127 GLN
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  197 MET
Chi-restraints excluded: chain B residue  216 LYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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
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 = 0.3725 r_free = 0.3725 target = 0.135195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.105329 restraints weight = 9389.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.02
r_work: 0.3169 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3424

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= 0.142
  Angle     :  0.497   5.487   8568  Z= 0.264
  Chirality :  0.037   0.124   1000
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.317  14.395    820
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 17.73 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.77 (0.30), residues: 736
  helix:  2.39 (0.19), residues: 606
  sheet:  None (None), residues: 0
  loop : -0.91 (0.58), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  54 
 HIS   0.005   0.001   HIS A 151 
 PHE   0.014   0.001   PHE B 181 
 TYR   0.020   0.001   TYR A 101 
 ARG   0.009   0.001   ARG A  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  502)
  hydrogen bonds       : angle       3.55372 ( 1494)
  SS BOND              : bond        0.00317 (    2)
  SS BOND              : angle       0.92887 (    4)
  covalent geometry    : bond        0.00334 ( 6320)
  covalent geometry    : angle       0.49669 ( 8564)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5245.48 seconds
wall clock time: 91 minutes 43.61 seconds (5503.61 seconds total)