Starting phenix.real_space_refine
on Wed Jul 23 17:32:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wn0_32618/07_2025/7wn0_32618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wn0_32618/07_2025/7wn0_32618.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wn0_32618/07_2025/7wn0_32618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wn0_32618/07_2025/7wn0_32618.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wn0_32618/07_2025/7wn0_32618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wn0_32618/07_2025/7wn0_32618.cif"
  }
  resolution = 3.64
  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=   0.001 sd=   0.028
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      26      5.16       5
     C    2553      2.51       5
     N     617      2.21       5
     O     683      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3879
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2953
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 11, 'TRANS': 359}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 926
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
  Time building chain proxies: 3.17, per 1000 atoms: 0.82
  Number of scatterers: 3879
  At special positions: 0
  Unit cell: (112.05, 57.27, 61.42, 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      26     16.00
     O     683      8.00
     N     617      7.00
     C    2553      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " 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: 0.95
  Conformation dependent library (CDL) restraints added in 471.7 milliseconds
  

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  920

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 3 sheets defined
      61.7% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 59
      removed outlier: 4.516A  pdb=" N   VAL A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   TRP A  53 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 83
      removed outlier: 3.887A  pdb=" N   PHE A  82 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 111
    Processing helix  chain 'A' and resid 112 through 144
    Processing helix  chain 'A' and resid 149 through 173
      removed outlier: 4.389A  pdb=" N   GLN A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 210
    Processing helix  chain 'A' and resid 231 through 239
    Processing helix  chain 'A' and resid 239 through 257
      removed outlier: 3.802A  pdb=" N   ILE A 243 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL A 249 " --> pdb=" O   THR A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 270
    Processing helix  chain 'A' and resid 272 through 282
      removed outlier: 3.752A  pdb=" N   ILE A 278 " --> pdb=" O   TYR A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 290
      removed outlier: 4.284A  pdb=" N   PHE A 288 " --> pdb=" O   GLN A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 320
      removed outlier: 3.678A  pdb=" N   VAL A 314 " --> pdb=" O   ASN A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 329
      removed outlier: 3.769A  pdb=" N   TRP A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 369
      removed outlier: 3.519A  pdb=" N   LEU A 350 " --> pdb=" O   CYS A 346 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   PHE A 357 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 360 " --> pdb=" O   TRP A 356 " (cutoff:3.500A)
      Proline residue:  A 361  - end of helix
      removed outlier: 5.247A  pdb=" N   VAL A 366 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   LYS A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU A 368 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 399
      removed outlier: 3.611A  pdb=" N   GLU A 379 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   TRP A 398 " --> pdb=" O   PHE A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 406
      removed outlier: 4.005A  pdb=" N   LEU A 405 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   PHE A 406 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 401 through 406'
    Processing helix  chain 'B' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13
      removed outlier: 3.716A  pdb=" N   SER B 122 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   VAL B  33 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 5.637A  pdb=" N   ARG B  38 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   LEU B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13
      removed outlier: 3.716A  pdb=" N   SER B 122 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)

    259 hydrogen bonds defined for protein.
    753 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: 1.12

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1176
        1.34 -     1.46: 999
        1.46 -     1.58: 1757
        1.58 -     1.70: 0
        1.70 -     1.82: 39
  Bond restraints: 3971
  Sorted by residual:
  bond pdb=" N   TYR B 103 "
       pdb=" CA  TYR B 103 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.35e-02 5.49e+03 8.72e+00
  bond pdb=" CG  PRO A 258 "
       pdb=" CD  PRO A 258 "
    ideal  model  delta    sigma   weight residual
    1.503  1.539 -0.036 3.40e-02 8.65e+02 1.11e+00
  bond pdb=" CA  VAL B  48 "
       pdb=" CB  VAL B  48 "
    ideal  model  delta    sigma   weight residual
    1.545  1.538  0.007 9.10e-03 1.21e+04 6.63e-01
  bond pdb=" CB  ASP A 333 "
       pdb=" CG  ASP A 333 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 2.50e-02 1.60e+03 5.84e-01
  bond pdb=" CB  LEU A  44 "
       pdb=" CG  LEU A  44 "
    ideal  model  delta    sigma   weight residual
    1.530  1.515  0.015 2.00e-02 2.50e+03 5.74e-01
  ... (remaining 3966 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 5317
        1.91 -     3.83: 56
        3.83 -     5.74: 12
        5.74 -     7.65: 5
        7.65 -     9.56: 1
  Bond angle restraints: 5391
  Sorted by residual:
  angle pdb=" CA  PRO A 258 "
        pdb=" N   PRO A 258 "
        pdb=" CD  PRO A 258 "
      ideal   model   delta    sigma   weight residual
     112.00  107.92    4.08 1.40e+00 5.10e-01 8.51e+00
  angle pdb=" CA  LEU A 201 "
        pdb=" CB  LEU A 201 "
        pdb=" CG  LEU A 201 "
      ideal   model   delta    sigma   weight residual
     116.30  125.86   -9.56 3.50e+00 8.16e-02 7.47e+00
  angle pdb=" N   TYR B 103 "
        pdb=" CA  TYR B 103 "
        pdb=" C   TYR B 103 "
      ideal   model   delta    sigma   weight residual
     112.87  110.07    2.80 1.20e+00 6.94e-01 5.43e+00
  angle pdb=" CB  MET A 233 "
        pdb=" CG  MET A 233 "
        pdb=" SD  MET A 233 "
      ideal   model   delta    sigma   weight residual
     112.70  119.59   -6.89 3.00e+00 1.11e-01 5.27e+00
  angle pdb=" N   SER A 308 "
        pdb=" CA  SER A 308 "
        pdb=" C   SER A 308 "
      ideal   model   delta    sigma   weight residual
     107.88  110.66   -2.78 1.41e+00 5.03e-01 3.87e+00
  ... (remaining 5386 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 1943
       17.13 -    34.27: 278
       34.27 -    51.40: 74
       51.40 -    68.54: 8
       68.54 -    85.67: 2
  Dihedral angle restraints: 2305
    sinusoidal: 875
      harmonic: 1430
  Sorted by residual:
  dihedral pdb=" CA  HIS A 334 "
           pdb=" C   HIS A 334 "
           pdb=" N   PRO A 335 "
           pdb=" CA  PRO A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.76  -20.24     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  ASN A 148 "
           pdb=" CB  ASN A 148 "
           pdb=" CG  ASN A 148 "
           pdb=" OD1 ASN A 148 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -163.46   73.46     2      2.00e+01 2.50e-03 1.10e+01
  dihedral pdb=" CG  ARG B  66 "
           pdb=" CD  ARG B  66 "
           pdb=" NE  ARG B  66 "
           pdb=" CZ  ARG B  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.39  -44.61     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 2302 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 354
       0.028 -    0.056: 174
       0.056 -    0.085: 69
       0.085 -    0.113: 27
       0.113 -    0.141: 4
  Chirality restraints: 628
  Sorted by residual:
  chirality pdb=" CA  PRO A 335 "
            pdb=" N   PRO A 335 "
            pdb=" C   PRO A 335 "
            pdb=" CB  PRO A 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.97e-01
  chirality pdb=" CA  TYR B 105 "
            pdb=" N   TYR B 105 "
            pdb=" C   TYR B 105 "
            pdb=" CB  TYR B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  VAL A 183 "
            pdb=" N   VAL A 183 "
            pdb=" C   VAL A 183 "
            pdb=" CB  VAL A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 625 not shown)

  Planarity restraints: 663
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 257 "   -0.065 5.00e-02 4.00e+02   9.76e-02 1.52e+01
        pdb=" N   PRO A 258 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO A 258 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 258 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 293 "    0.035 5.00e-02 4.00e+02   5.24e-02 4.40e+00
        pdb=" N   PRO A 294 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 294 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 294 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 119 "    0.009 2.00e-02 2.50e+03   1.81e-02 3.28e+00
        pdb=" C   TYR A 119 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   TYR A 119 "    0.012 2.00e-02 2.50e+03
        pdb=" N   CYS A 120 "    0.011 2.00e-02 2.50e+03
  ... (remaining 660 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1043
        2.80 -     3.32: 3846
        3.32 -     3.85: 6520
        3.85 -     4.37: 7483
        4.37 -     4.90: 13006
  Nonbonded interactions: 31898
  Sorted by model distance:
  nonbonded pdb=" N   GLU B  88 "
            pdb=" OE1 GLU B  88 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" N   GLU A 146 "
            pdb=" OE1 GLU A 146 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" OG1 THR A 253 "
            pdb=" NH2 ARG A 319 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" N   GLN B  44 "
            pdb=" OE1 GLN B  44 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" O   SER B 102 "
            pdb=" OG  SER B 102 "
     model   vdw
     2.325 3.040
  ... (remaining 31893 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             2.780
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.630
  Find NCS groups from input model:        0.030
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3972  Z= 0.144
  Angle     :  0.572   9.565   5393  Z= 0.296
  Chirality :  0.041   0.141    628
  Planarity :  0.005   0.098    663
  Dihedral  : 16.818  85.672   1382
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 28.44 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.10 (0.39), residues: 488
  helix:  1.00 (0.32), residues: 278
  sheet:  1.61 (0.73), residues: 56
  loop :  0.07 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 356 
 HIS   0.010   0.001   HIS A 334 
 PHE   0.012   0.001   PHE A  82 
 TYR   0.015   0.001   TYR A 119 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20741 (  254)
  hydrogen bonds       : angle       7.36356 (  753)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.10138 (    2)
  covalent geometry    : bond        0.00309 ( 3971)
  covalent geometry    : angle       0.57208 ( 5391)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 76
  average time/residue: 0.1428
  time to fit residues: 13.9944
Evaluate side-chains
  77 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:    0.0870
   chunk 37 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.9564

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

Flipped N/Q/H residues before XYZ refinement:
A  66 ASN
A 135 GLN
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 GLN
A 284 GLN
A 316 ASN
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 ASN ** 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 = 0.3343 r_free = 0.3343 target = 0.119787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.097602 restraints weight = 5495.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.100243 restraints weight = 3294.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.101853 restraints weight = 2422.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3972  Z= 0.174
  Angle     :  0.597   8.021   5393  Z= 0.312
  Chirality :  0.043   0.129    628
  Planarity :  0.005   0.054    663
  Dihedral  :  4.556  34.673    521
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 25.87 %
    Favored  : 69.46 %
  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:  1.36 (0.39), residues: 488
  helix:  1.29 (0.31), residues: 285
  sheet:  1.16 (0.62), residues: 69
  loop :  0.09 (0.57), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 356 
 HIS   0.007   0.001   HIS A 334 
 PHE   0.014   0.001   PHE A  36 
 TYR   0.014   0.002   TYR A 119 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05667 (  254)
  hydrogen bonds       : angle       5.10692 (  753)
  SS BOND              : bond        0.00098 (    1)
  SS BOND              : angle       0.31658 (    2)
  covalent geometry    : bond        0.00400 ( 3971)
  covalent geometry    : angle       0.59673 ( 5391)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6679 (mt)
REVERT: B   55 ASP cc_start: 0.7559 (t0) cc_final: 0.7221 (t0)
  outliers start: 20
  outliers final: 13
  residues processed: 89
  average time/residue: 0.1706
  time to fit residues: 19.7279
Evaluate side-chains
  89 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  123 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 148 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.121625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.099800 restraints weight = 5383.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.102553 restraints weight = 3255.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.104189 restraints weight = 2384.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.1366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3972  Z= 0.153
  Angle     :  0.570   7.937   5393  Z= 0.294
  Chirality :  0.042   0.125    628
  Planarity :  0.004   0.050    663
  Dihedral  :  4.214  33.284    519
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 25.17 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.46 (0.39), residues: 488
  helix:  1.45 (0.31), residues: 285
  sheet:  0.92 (0.57), residues: 71
  loop :  0.10 (0.58), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 356 
 HIS   0.006   0.001   HIS A 334 
 PHE   0.008   0.001   PHE A 365 
 TYR   0.019   0.001   TYR B  37 
 ARG   0.002   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05144 (  254)
  hydrogen bonds       : angle       4.76270 (  753)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       0.11010 (    2)
  covalent geometry    : bond        0.00348 ( 3971)
  covalent geometry    : angle       0.56969 ( 5391)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6664 (mt)
REVERT: B   55 ASP cc_start: 0.7657 (t0) cc_final: 0.7276 (t0)
  outliers start: 24
  outliers final: 15
  residues processed: 95
  average time/residue: 0.1829
  time to fit residues: 21.8310
Evaluate side-chains
  93 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  123 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 43 optimal weight:    0.1980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 148 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.125421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.103171 restraints weight = 5298.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.106231 restraints weight = 3048.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.108067 restraints weight = 2179.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3972  Z= 0.152
  Angle     :  0.595   7.840   5393  Z= 0.305
  Chirality :  0.042   0.124    628
  Planarity :  0.004   0.049    663
  Dihedral  :  4.194  32.868    519
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 26.11 %
    Favored  : 67.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.41 (0.39), residues: 488
  helix:  1.44 (0.31), residues: 285
  sheet:  0.76 (0.56), residues: 71
  loop :  0.13 (0.59), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 251 
 HIS   0.005   0.001   HIS A 334 
 PHE   0.009   0.001   PHE A  82 
 TYR   0.014   0.001   TYR A 119 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04947 (  254)
  hydrogen bonds       : angle       4.63633 (  753)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.09388 (    2)
  covalent geometry    : bond        0.00347 ( 3971)
  covalent geometry    : angle       0.59522 ( 5391)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6604 (mt)
REVERT: B   55 ASP cc_start: 0.7650 (t0) cc_final: 0.7246 (t0)
  outliers start: 26
  outliers final: 20
  residues processed: 97
  average time/residue: 0.1422
  time to fit residues: 17.5795
Evaluate side-chains
  98 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  117 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 ASN
** B 110 ASN ** 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 = 0.3377 r_free = 0.3377 target = 0.122091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.099655 restraints weight = 5519.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.102517 restraints weight = 3160.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.104522 restraints weight = 2270.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3972  Z= 0.192
  Angle     :  0.651  10.631   5393  Z= 0.325
  Chirality :  0.044   0.127    628
  Planarity :  0.004   0.048    663
  Dihedral  :  4.280  32.815    519
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  6.99 %
    Allowed  : 25.41 %
    Favored  : 67.60 %
  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:  1.14 (0.38), residues: 488
  helix:  1.22 (0.30), residues: 291
  sheet:  0.75 (0.55), residues: 71
  loop : -0.13 (0.58), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A 334 
 PHE   0.009   0.001   PHE A  63 
 TYR   0.018   0.001   TYR B  37 
 ARG   0.004   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05079 (  254)
  hydrogen bonds       : angle       4.66134 (  753)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.06323 (    2)
  covalent geometry    : bond        0.00462 ( 3971)
  covalent geometry    : angle       0.65157 ( 5391)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6781 (mt)
REVERT: B   55 ASP cc_start: 0.7716 (t0) cc_final: 0.7250 (t0)
REVERT: B  105 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.5650 (p90)
  outliers start: 30
  outliers final: 23
  residues processed: 97
  average time/residue: 0.1353
  time to fit residues: 16.9240
Evaluate side-chains
  100 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  115 GLN
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  117 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0770
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 148 ASN
A 209 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.125653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.103252 restraints weight = 5349.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.106331 restraints weight = 3065.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.108205 restraints weight = 2189.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3972  Z= 0.141
  Angle     :  0.605   8.505   5393  Z= 0.305
  Chirality :  0.042   0.131    628
  Planarity :  0.004   0.048    663
  Dihedral  :  4.240  33.302    519
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 26.34 %
    Favored  : 68.07 %
  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:  1.25 (0.38), residues: 488
  helix:  1.44 (0.31), residues: 285
  sheet:  0.92 (0.56), residues: 69
  loop : -0.43 (0.56), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 334 
 PHE   0.007   0.001   PHE A  42 
 TYR   0.014   0.001   TYR A 119 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04718 (  254)
  hydrogen bonds       : angle       4.56388 (  753)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.14977 (    2)
  covalent geometry    : bond        0.00316 ( 3971)
  covalent geometry    : angle       0.60518 ( 5391)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6615 (mt)
REVERT: B   55 ASP cc_start: 0.7668 (t0) cc_final: 0.7228 (t0)
REVERT: B  105 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.5723 (p90)
REVERT: B  118 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8186 (tp-100)
  outliers start: 24
  outliers final: 18
  residues processed: 92
  average time/residue: 0.1303
  time to fit residues: 15.5270
Evaluate side-chains
  96 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  209 ASN
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  105 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0370
   chunk 23 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 209 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** 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 = 0.3395 r_free = 0.3395 target = 0.123656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.101386 restraints weight = 5361.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.104445 restraints weight = 3069.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.106307 restraints weight = 2182.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3972  Z= 0.144
  Angle     :  0.619   7.959   5393  Z= 0.310
  Chirality :  0.042   0.126    628
  Planarity :  0.004   0.047    663
  Dihedral  :  4.192  32.950    519
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 27.74 %
    Favored  : 67.37 %
  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:  1.23 (0.38), residues: 488
  helix:  1.39 (0.31), residues: 286
  sheet:  0.97 (0.56), residues: 69
  loop : -0.41 (0.56), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 334 
 PHE   0.013   0.001   PHE A 116 
 TYR   0.014   0.001   TYR A 240 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04698 (  254)
  hydrogen bonds       : angle       4.48111 (  753)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       0.08676 (    2)
  covalent geometry    : bond        0.00328 ( 3971)
  covalent geometry    : angle       0.61881 ( 5391)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6596 (mt)
REVERT: B   55 ASP cc_start: 0.7653 (t0) cc_final: 0.7207 (t0)
REVERT: B  105 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.5655 (p90)
REVERT: B  118 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8168 (tp-100)
  outliers start: 21
  outliers final: 15
  residues processed: 91
  average time/residue: 0.1264
  time to fit residues: 14.8499
Evaluate side-chains
  93 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  105 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 32 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 148 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.122607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.100108 restraints weight = 5361.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.102932 restraints weight = 3088.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.104969 restraints weight = 2229.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3972  Z= 0.149
  Angle     :  0.618   7.965   5393  Z= 0.309
  Chirality :  0.042   0.127    628
  Planarity :  0.004   0.048    663
  Dihedral  :  4.165  32.620    519
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 27.74 %
    Favored  : 67.37 %
  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:  1.22 (0.38), residues: 488
  helix:  1.40 (0.31), residues: 286
  sheet:  0.82 (0.56), residues: 71
  loop : -0.37 (0.57), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 262 
 PHE   0.010   0.001   PHE A 116 
 TYR   0.014   0.001   TYR B  98 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04707 (  254)
  hydrogen bonds       : angle       4.43594 (  753)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.07149 (    2)
  covalent geometry    : bond        0.00345 ( 3971)
  covalent geometry    : angle       0.61767 ( 5391)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.8205 (tpp) cc_final: 0.7988 (tpp)
REVERT: A   93 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6614 (mt)
REVERT: B   55 ASP cc_start: 0.7684 (t0) cc_final: 0.7223 (t0)
REVERT: B  105 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.5656 (p90)
  outliers start: 21
  outliers final: 15
  residues processed: 90
  average time/residue: 0.1389
  time to fit residues: 16.1405
Evaluate side-chains
  95 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  105 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 44 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
A 148 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 118 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.122942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.100007 restraints weight = 5483.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.102846 restraints weight = 3186.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.104819 restraints weight = 2316.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3972  Z= 0.157
  Angle     :  0.632   8.022   5393  Z= 0.316
  Chirality :  0.043   0.129    628
  Planarity :  0.004   0.047    663
  Dihedral  :  4.191  32.423    519
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 28.44 %
    Favored  : 67.13 %
  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:  1.29 (0.38), residues: 488
  helix:  1.44 (0.31), residues: 285
  sheet:  1.07 (0.58), residues: 69
  loop : -0.43 (0.56), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 262 
 PHE   0.009   0.001   PHE A 116 
 TYR   0.015   0.001   TYR A 240 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04721 (  254)
  hydrogen bonds       : angle       4.42458 (  753)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.12538 (    2)
  covalent geometry    : bond        0.00365 ( 3971)
  covalent geometry    : angle       0.63208 ( 5391)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6629 (mt)
REVERT: B   55 ASP cc_start: 0.7720 (t0) cc_final: 0.7233 (t0)
REVERT: B  105 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.5666 (p90)
  outliers start: 19
  outliers final: 15
  residues processed: 85
  average time/residue: 0.1291
  time to fit residues: 14.4004
Evaluate side-chains
  92 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  105 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 25 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.123236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.100161 restraints weight = 5509.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.103138 restraints weight = 3204.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.104982 restraints weight = 2317.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3972  Z= 0.150
  Angle     :  0.621   8.000   5393  Z= 0.310
  Chirality :  0.042   0.128    628
  Planarity :  0.004   0.047    663
  Dihedral  :  4.136  32.301    519
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 29.14 %
    Favored  : 67.13 %
  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:  1.24 (0.38), residues: 488
  helix:  1.43 (0.31), residues: 286
  sheet:  0.84 (0.57), residues: 71
  loop : -0.41 (0.57), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 262 
 PHE   0.009   0.001   PHE A 116 
 TYR   0.013   0.001   TYR B  98 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04686 (  254)
  hydrogen bonds       : angle       4.39404 (  753)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       0.09466 (    2)
  covalent geometry    : bond        0.00348 ( 3971)
  covalent geometry    : angle       0.62125 ( 5391)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A   37 MET cc_start: 0.8265 (tpp) cc_final: 0.8045 (tpp)
REVERT: A   93 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6615 (mt)
REVERT: B   55 ASP cc_start: 0.7749 (t0) cc_final: 0.7285 (t0)
REVERT: B  105 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.5618 (p90)
  outliers start: 16
  outliers final: 14
  residues processed: 87
  average time/residue: 0.1231
  time to fit residues: 14.0654
Evaluate side-chains
  92 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  105 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   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 135 GLN
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.122035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.099289 restraints weight = 5419.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.102151 restraints weight = 3177.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.103888 restraints weight = 2311.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3972  Z= 0.166
  Angle     :  0.647   8.051   5393  Z= 0.325
  Chirality :  0.043   0.130    628
  Planarity :  0.004   0.047    663
  Dihedral  :  4.160  32.136    519
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 28.44 %
    Favored  : 67.60 %
  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:  1.22 (0.38), residues: 488
  helix:  1.41 (0.31), residues: 285
  sheet:  0.93 (0.57), residues: 69
  loop : -0.45 (0.56), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 262 
 PHE   0.009   0.001   PHE A 116 
 TYR   0.015   0.001   TYR A 240 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04781 (  254)
  hydrogen bonds       : angle       4.41988 (  753)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.06843 (    2)
  covalent geometry    : bond        0.00393 ( 3971)
  covalent geometry    : angle       0.64747 ( 5391)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1641.07 seconds
wall clock time: 29 minutes 45.46 seconds (1785.46 seconds total)