Starting phenix.real_space_refine
on Fri May  9 18:43:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bll_44666/05_2025/9bll_44666_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bll_44666/05_2025/9bll_44666.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bll_44666/05_2025/9bll_44666.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bll_44666/05_2025/9bll_44666.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bll_44666/05_2025/9bll_44666_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bll_44666/05_2025/9bll_44666_neut.cif"
  }
  resolution = 4.1
  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=   0.009
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      14      5.16       5
     C    2175      2.51       5
     N     578      2.21       5
     O     661      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3428
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "L"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 811
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 101}
    Chain: "T"
      Number of atoms: 1605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1605
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 14, 'TRANS': 188}
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "T"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.22, per 1000 atoms: 0.94
  Number of scatterers: 3428
  At special positions: 0
  Unit cell: (70.6457, 72.4342, 104.627, 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      14     16.00
     O     661      8.00
     N     578      7.00
     C    2175      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS T 336 " - pdb=" SG  CYS T 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS T 379 " - pdb=" SG  CYS T 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS T 391 " - pdb=" SG  CYS T 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS T 480 " - pdb=" SG  CYS T 488 " 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
  Links applied
    BETA1-4
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG G   1 " - " ASN H 105 "
      " NAG T1301 " - " ASN T 343 "
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 432.3 milliseconds
  

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  794

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 8 sheets defined
      9.3% alpha, 26.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.662A  pdb=" N   THR H  87 " --> pdb=" O   SER H  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 99 through 104
      removed outlier: 3.961A  pdb=" N   LEU H 104 " --> pdb=" O   GLY H 100 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
    Processing helix  chain 'T' and resid 364 through 371
      removed outlier: 3.623A  pdb=" N   PHE T 371 " --> pdb=" O   ILE T 368 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 384 through 388
      removed outlier: 4.493A  pdb=" N   ASN T 388 " --> pdb=" O   THR T 385 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 405 through 410
      removed outlier: 5.004A  pdb=" N   SER T 408 " --> pdb=" O   ASN T 405 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 5.848A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 18 through 21
    Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 24
    Processing sheet with id=AA4, first strand: chain 'L' and resid 45 through 48
      removed outlier: 6.463A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 45 through 48
      removed outlier: 6.463A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'T' and resid 356 through 358
      removed outlier: 3.977A  pdb=" N   ASN T 394 " --> pdb=" O   GLU T 516 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU T 516 " --> pdb=" O   ASN T 394 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'T' and resid 361 through 362
      removed outlier: 7.235A  pdb=" N   CYS T 361 " --> pdb=" O   CYS T 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'T' and resid 452 through 454

    100 hydrogen bonds defined for protein.
    222 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.82

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1103
        1.35 -     1.48: 978
        1.48 -     1.61: 1421
        1.61 -     1.74: 0
        1.74 -     1.87: 16
  Bond restraints: 3518
  Sorted by residual:
  bond pdb=" C   ILE H  52 "
       pdb=" N   PRO H  52A"
    ideal  model  delta    sigma   weight residual
    1.336  1.297  0.039 1.20e-02 6.94e+03 1.05e+01
  bond pdb=" N   VAL T 433 "
       pdb=" CA  VAL T 433 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.11e+00
  bond pdb=" N   VAL L  95 "
       pdb=" CA  VAL L  95 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 8.03e+00
  bond pdb=" N   GLY T 431 "
       pdb=" CA  GLY T 431 "
    ideal  model  delta    sigma   weight residual
    1.448  1.480 -0.033 1.18e-02 7.18e+03 7.82e+00
  bond pdb=" N   CYS T 432 "
       pdb=" CA  CYS T 432 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.25e-02 6.40e+03 6.66e+00
  ... (remaining 3513 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 4466
        1.53 -     3.07: 267
        3.07 -     4.60: 46
        4.60 -     6.14: 13
        6.14 -     7.67: 3
  Bond angle restraints: 4795
  Sorted by residual:
  angle pdb=" CA  GLY T 431 "
        pdb=" C   GLY T 431 "
        pdb=" O   GLY T 431 "
      ideal   model   delta    sigma   weight residual
     122.13  117.67    4.46 8.90e-01 1.26e+00 2.51e+01
  angle pdb=" N   GLY H 100 "
        pdb=" CA  GLY H 100 "
        pdb=" C   GLY H 100 "
      ideal   model   delta    sigma   weight residual
     113.24  118.50   -5.26 1.31e+00 5.83e-01 1.61e+01
  angle pdb=" C   SER H  96 "
        pdb=" N   TYR H  97 "
        pdb=" CA  TYR H  97 "
      ideal   model   delta    sigma   weight residual
     121.54  114.01    7.53 1.91e+00 2.74e-01 1.56e+01
  angle pdb=" N   ASP H  98 "
        pdb=" CA  ASP H  98 "
        pdb=" C   ASP H  98 "
      ideal   model   delta    sigma   weight residual
     110.80  118.47   -7.67 2.13e+00 2.20e-01 1.30e+01
  angle pdb=" CA  GLY T 431 "
        pdb=" C   GLY T 431 "
        pdb=" N   CYS T 432 "
      ideal   model   delta    sigma   weight residual
     114.50  118.51   -4.01 1.16e+00 7.43e-01 1.20e+01
  ... (remaining 4790 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.83: 1867
       16.83 -    33.65: 201
       33.65 -    50.47: 36
       50.47 -    67.29: 3
       67.29 -    84.12: 3
  Dihedral angle restraints: 2110
    sinusoidal: 849
      harmonic: 1261
  Sorted by residual:
  dihedral pdb=" CA  TYR H 108 "
           pdb=" C   TYR H 108 "
           pdb=" N   TYR H 109 "
           pdb=" CA  TYR H 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.03  -22.97     0      5.00e+00 4.00e-02 2.11e+01
  dihedral pdb=" CA  TYR H  74 "
           pdb=" C   TYR H  74 "
           pdb=" N   ALA H  75 "
           pdb=" CA  ALA H  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.13  -22.87     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  TYR H  99 "
           pdb=" C   TYR H  99 "
           pdb=" N   GLY H 100 "
           pdb=" CA  GLY H 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.41  -21.59     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 2107 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 477
       0.104 -    0.207: 46
       0.207 -    0.311: 3
       0.311 -    0.415: 0
       0.415 -    0.518: 1
  Chirality restraints: 527
  Sorted by residual:
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN H 105 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.88   -0.52 2.00e-01 2.50e+01 6.72e+00
  chirality pdb=" CB  ILE H  52 "
            pdb=" CA  ILE H  52 "
            pdb=" CG1 ILE H  52 "
            pdb=" CG2 ILE H  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  ILE T 434 "
            pdb=" N   ILE T 434 "
            pdb=" C   ILE T 434 "
            pdb=" CB  ILE T 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 524 not shown)

  Planarity restraints: 624
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR T 430 "   -0.021 2.00e-02 2.50e+03   4.21e-02 1.77e+01
        pdb=" C   THR T 430 "    0.073 2.00e-02 2.50e+03
        pdb=" O   THR T 430 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   GLY T 431 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE H  52 "   -0.039 5.00e-02 4.00e+02   5.80e-02 5.38e+00
        pdb=" N   PRO H  52A"    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO H  52A"   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO H  52A"   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 106 "    0.015 2.00e-02 2.50e+03   1.57e-02 4.94e+00
        pdb=" CG  TYR H 106 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 106 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 106 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 106 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 106 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 106 "    0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR H 106 "    0.003 2.00e-02 2.50e+03
  ... (remaining 621 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 112
        2.67 -     3.22: 3492
        3.22 -     3.78: 5121
        3.78 -     4.34: 6751
        4.34 -     4.90: 10861
  Nonbonded interactions: 26337
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG L  54 "
            pdb=" O   PRO L  59 "
     model   vdw
     2.108 3.120
  nonbonded pdb=" OG  SER T 359 "
            pdb=" OD1 ASN T 394 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" NH1 ARG L  54 "
            pdb=" O   ILE L  58 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" OE2 GLU H   6 "
            pdb=" N   GLY H 117 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" O   GLY H  30 "
            pdb=" OG  SER H  31 "
     model   vdw
     2.218 3.040
  ... (remaining 26332 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:             3.950
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     13.160
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
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      :  0.007   0.083   3527  Z= 0.333
  Angle     :  0.878   9.878   4816  Z= 0.481
  Chirality :  0.064   0.518    527
  Planarity :  0.006   0.058    622
  Dihedral  : 13.881  84.118   1298
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 23.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.87 %
    Favored  : 87.13 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.82 %
    Favored  : 98.91 %
  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: -2.86 (0.40), residues: 435
  helix: -4.49 (0.52), residues: 22
  sheet: -1.50 (0.45), residues: 125
  loop : -1.95 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP H  36 
 HIS   0.005   0.002   HIS T 505 
 PHE   0.023   0.003   PHE T 371 
 TYR   0.034   0.003   TYR H 106 
 ARG   0.005   0.001   ARG L  27 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00484 (    2)
  link_NAG-ASN         : angle       5.33327 (    6)
  link_BETA1-4         : bond        0.00206 (    1)
  link_BETA1-4         : angle       3.66612 (    3)
  hydrogen bonds       : bond        0.14908 (   91)
  hydrogen bonds       : angle       7.81201 (  222)
  SS BOND              : bond        0.00438 (    6)
  SS BOND              : angle       1.39834 (   12)
  covalent geometry    : bond        0.00721 ( 3518)
  covalent geometry    : angle       0.85151 ( 4795)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: H   86 ASP cc_start: 0.7636 (m-30) cc_final: 0.7423 (m-30)
REVERT: H  111 MET cc_start: 0.8687 (mpp) cc_final: 0.8357 (mpp)
REVERT: H  112 ASP cc_start: 0.9256 (t70) cc_final: 0.9013 (t0)
REVERT: L   47 LEU cc_start: 0.8999 (mt) cc_final: 0.8739 (mt)
REVERT: L   95 VAL cc_start: 0.8149 (m) cc_final: 0.7762 (m)
REVERT: T  396 TYR cc_start: 0.8519 (m-80) cc_final: 0.8225 (m-80)
REVERT: T  473 TYR cc_start: 0.8233 (t80) cc_final: 0.8024 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 110
  average time/residue: 0.1507
  time to fit residues: 20.3287
Evaluate side-chains
  95 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
** L  51 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 = 0.3851 r_free = 0.3851 target = 0.161614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.128836 restraints weight = 5969.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.132622 restraints weight = 3884.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.135263 restraints weight = 2859.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3527  Z= 0.165
  Angle     :  0.747   9.482   4816  Z= 0.371
  Chirality :  0.055   0.304    527
  Planarity :  0.005   0.045    622
  Dihedral  :  7.429  49.376    551
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  4.64 %
    Favored  : 94.81 %
  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 (0.41), residues: 435
  helix: -4.73 (0.39), residues: 22
  sheet: -1.42 (0.46), residues: 127
  loop : -1.65 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H  36 
 HIS   0.003   0.001   HIS T 505 
 PHE   0.016   0.002   PHE T 429 
 TYR   0.014   0.002   TYR T 351 
 ARG   0.003   0.000   ARG L  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00755 (    2)
  link_NAG-ASN         : angle       5.06853 (    6)
  link_BETA1-4         : bond        0.00515 (    1)
  link_BETA1-4         : angle       2.20782 (    3)
  hydrogen bonds       : bond        0.03932 (   91)
  hydrogen bonds       : angle       6.55494 (  222)
  SS BOND              : bond        0.00169 (    6)
  SS BOND              : angle       0.90326 (   12)
  covalent geometry    : bond        0.00391 ( 3518)
  covalent geometry    : angle       0.72290 ( 4795)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.9046 (m100) cc_final: 0.8750 (m100)
REVERT: H   59 TYR cc_start: 0.8273 (m-80) cc_final: 0.8011 (m-80)
REVERT: H   83 ARG cc_start: 0.7420 (mtm110) cc_final: 0.7114 (mtm110)
REVERT: H   86 ASP cc_start: 0.7738 (m-30) cc_final: 0.7273 (m-30)
REVERT: H  112 ASP cc_start: 0.9182 (t70) cc_final: 0.8953 (t0)
REVERT: L   47 LEU cc_start: 0.8854 (mt) cc_final: 0.8580 (mt)
REVERT: L   95 VAL cc_start: 0.8252 (m) cc_final: 0.7761 (m)
REVERT: T  396 TYR cc_start: 0.8544 (m-80) cc_final: 0.8317 (m-80)
REVERT: T  418 ILE cc_start: 0.9502 (tp) cc_final: 0.9230 (tt)
REVERT: T  516 GLU cc_start: 0.6694 (tp30) cc_final: 0.6390 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1430
  time to fit residues: 19.6561
Evaluate side-chains
  94 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0770
   chunk 15 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.161877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.128641 restraints weight = 6000.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.132703 restraints weight = 3798.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.135531 restraints weight = 2738.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3527  Z= 0.160
  Angle     :  0.719   8.925   4816  Z= 0.356
  Chirality :  0.054   0.300    527
  Planarity :  0.005   0.045    622
  Dihedral  :  7.157  49.054    551
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  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: -2.46 (0.41), residues: 435
  helix: -4.66 (0.45), residues: 22
  sheet: -1.10 (0.48), residues: 122
  loop : -1.69 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP T 436 
 HIS   0.003   0.001   HIS L  38 
 PHE   0.013   0.002   PHE T 429 
 TYR   0.019   0.002   TYR T 489 
 ARG   0.002   0.000   ARG L  27 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00521 (    2)
  link_NAG-ASN         : angle       4.90419 (    6)
  link_BETA1-4         : bond        0.00240 (    1)
  link_BETA1-4         : angle       2.08737 (    3)
  hydrogen bonds       : bond        0.03571 (   91)
  hydrogen bonds       : angle       6.14423 (  222)
  SS BOND              : bond        0.00137 (    6)
  SS BOND              : angle       0.78576 (   12)
  covalent geometry    : bond        0.00373 ( 3518)
  covalent geometry    : angle       0.69653 ( 4795)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   80 MET cc_start: 0.8902 (tmm) cc_final: 0.8700 (tmm)
REVERT: H   83 ARG cc_start: 0.7415 (mtm110) cc_final: 0.7214 (mtm110)
REVERT: H   86 ASP cc_start: 0.7654 (m-30) cc_final: 0.7027 (m-30)
REVERT: H  112 ASP cc_start: 0.9140 (t70) cc_final: 0.8921 (t0)
REVERT: L   47 LEU cc_start: 0.8887 (mt) cc_final: 0.8527 (mt)
REVERT: L   95 VAL cc_start: 0.8428 (m) cc_final: 0.8008 (m)
REVERT: T  396 TYR cc_start: 0.8553 (m-80) cc_final: 0.8295 (m-80)
REVERT: T  516 GLU cc_start: 0.6829 (tp30) cc_final: 0.6512 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1506
  time to fit residues: 20.8594
Evaluate side-chains
  102 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0870
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.164231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.130906 restraints weight = 5974.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.135048 restraints weight = 3757.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.137886 restraints weight = 2690.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3527  Z= 0.138
  Angle     :  0.710   9.170   4816  Z= 0.349
  Chirality :  0.053   0.302    527
  Planarity :  0.005   0.043    622
  Dihedral  :  6.887  48.852    551
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  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: -2.39 (0.41), residues: 435
  helix: -4.74 (0.40), residues: 28
  sheet: -1.03 (0.47), residues: 121
  loop : -1.55 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP T 436 
 HIS   0.002   0.001   HIS L  38 
 PHE   0.012   0.001   PHE T 429 
 TYR   0.014   0.002   TYR T 489 
 ARG   0.001   0.000   ARG H  94 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00626 (    2)
  link_NAG-ASN         : angle       5.00921 (    6)
  link_BETA1-4         : bond        0.00266 (    1)
  link_BETA1-4         : angle       2.12973 (    3)
  hydrogen bonds       : bond        0.03394 (   91)
  hydrogen bonds       : angle       6.05473 (  222)
  SS BOND              : bond        0.00154 (    6)
  SS BOND              : angle       0.71168 (   12)
  covalent geometry    : bond        0.00327 ( 3518)
  covalent geometry    : angle       0.68582 ( 4795)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   83 ARG cc_start: 0.7647 (mtm110) cc_final: 0.6959 (mtm110)
REVERT: H   86 ASP cc_start: 0.7749 (m-30) cc_final: 0.7116 (m-30)
REVERT: H  112 ASP cc_start: 0.9120 (t70) cc_final: 0.8895 (t0)
REVERT: L   47 LEU cc_start: 0.8881 (mt) cc_final: 0.8408 (mt)
REVERT: L   95 VAL cc_start: 0.8306 (m) cc_final: 0.7907 (m)
REVERT: T  396 TYR cc_start: 0.8610 (m-80) cc_final: 0.8347 (m-80)
REVERT: T  449 TYR cc_start: 0.9222 (m-80) cc_final: 0.9012 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1451
  time to fit residues: 20.1460
Evaluate side-chains
  102 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0020
   chunk 19 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.2980
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.164504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.131479 restraints weight = 5931.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.135754 restraints weight = 3663.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.138652 restraints weight = 2594.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3527  Z= 0.128
  Angle     :  0.700   9.022   4816  Z= 0.344
  Chirality :  0.054   0.300    527
  Planarity :  0.004   0.043    622
  Dihedral  :  6.765  49.470    551
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.91 %
    Favored  : 97.81 %
  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: -2.25 (0.41), residues: 435
  helix: -4.70 (0.44), residues: 28
  sheet: -0.90 (0.49), residues: 114
  loop : -1.46 (0.38), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  36 
 HIS   0.002   0.001   HIS L  38 
 PHE   0.012   0.001   PHE T 497 
 TYR   0.030   0.002   TYR T 501 
 ARG   0.001   0.000   ARG L  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00671 (    2)
  link_NAG-ASN         : angle       4.86448 (    6)
  link_BETA1-4         : bond        0.00480 (    1)
  link_BETA1-4         : angle       2.28231 (    3)
  hydrogen bonds       : bond        0.03260 (   91)
  hydrogen bonds       : angle       5.93591 (  222)
  SS BOND              : bond        0.00370 (    6)
  SS BOND              : angle       0.59978 (   12)
  covalent geometry    : bond        0.00304 ( 3518)
  covalent geometry    : angle       0.67747 ( 4795)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8997 (m100) cc_final: 0.8571 (m100)
REVERT: H   54 LEU cc_start: 0.9053 (mp) cc_final: 0.8148 (tt)
REVERT: H   83 ARG cc_start: 0.7572 (mtm110) cc_final: 0.6777 (mtm110)
REVERT: H   86 ASP cc_start: 0.7779 (m-30) cc_final: 0.7101 (m-30)
REVERT: H  112 ASP cc_start: 0.9109 (t70) cc_final: 0.8887 (t0)
REVERT: L    6 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6268 (pm20)
REVERT: L   33 VAL cc_start: 0.6940 (m) cc_final: 0.6674 (m)
REVERT: L   47 LEU cc_start: 0.8886 (mt) cc_final: 0.8432 (mt)
REVERT: L   95 VAL cc_start: 0.8474 (m) cc_final: 0.8083 (m)
REVERT: T  396 TYR cc_start: 0.8583 (m-80) cc_final: 0.8277 (m-80)
REVERT: T  449 TYR cc_start: 0.9196 (m-80) cc_final: 0.8985 (m-80)
REVERT: T  467 ASP cc_start: 0.7293 (t0) cc_final: 0.6696 (m-30)
REVERT: T  516 GLU cc_start: 0.6804 (tp30) cc_final: 0.6595 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1639
  time to fit residues: 22.7638
Evaluate side-chains
  99 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0770
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0470
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7840

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
** L  51 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 = 0.3873 r_free = 0.3873 target = 0.163952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.130391 restraints weight = 6045.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.134679 restraints weight = 3781.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.137558 restraints weight = 2708.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3527  Z= 0.160
  Angle     :  0.715   8.886   4816  Z= 0.351
  Chirality :  0.055   0.315    527
  Planarity :  0.004   0.043    622
  Dihedral  :  6.769  48.669    551
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  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: -2.27 (0.41), residues: 435
  helix: -4.73 (0.43), residues: 28
  sheet: -1.12 (0.47), residues: 123
  loop : -1.36 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  36 
 HIS   0.002   0.001   HIS L  38 
 PHE   0.010   0.002   PHE T 429 
 TYR   0.030   0.002   TYR T 501 
 ARG   0.002   0.000   ARG L  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00622 (    2)
  link_NAG-ASN         : angle       4.94181 (    6)
  link_BETA1-4         : bond        0.00354 (    1)
  link_BETA1-4         : angle       2.17718 (    3)
  hydrogen bonds       : bond        0.03358 (   91)
  hydrogen bonds       : angle       5.87495 (  222)
  SS BOND              : bond        0.00243 (    6)
  SS BOND              : angle       0.53397 (   12)
  covalent geometry    : bond        0.00384 ( 3518)
  covalent geometry    : angle       0.69253 ( 4795)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.389 
Fit side-chains
REVERT: H   54 LEU cc_start: 0.8918 (mp) cc_final: 0.8014 (tt)
REVERT: H   83 ARG cc_start: 0.7461 (mtm110) cc_final: 0.6810 (mtm110)
REVERT: H   86 ASP cc_start: 0.7760 (m-30) cc_final: 0.7069 (m-30)
REVERT: H  112 ASP cc_start: 0.9122 (t70) cc_final: 0.8900 (t0)
REVERT: L   33 VAL cc_start: 0.7060 (m) cc_final: 0.6821 (m)
REVERT: L   47 LEU cc_start: 0.8920 (mt) cc_final: 0.8516 (mt)
REVERT: L   95 VAL cc_start: 0.8393 (m) cc_final: 0.8125 (m)
REVERT: T  396 TYR cc_start: 0.8630 (m-80) cc_final: 0.8298 (m-80)
REVERT: T  449 TYR cc_start: 0.9225 (m-80) cc_final: 0.9006 (m-80)
REVERT: T  467 ASP cc_start: 0.7366 (t0) cc_final: 0.6726 (m-30)
REVERT: T  516 GLU cc_start: 0.6849 (tp30) cc_final: 0.6598 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1531
  time to fit residues: 20.7391
Evaluate side-chains
  103 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0570
   chunk 4 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0770
   chunk 5 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   overall best weight:    0.4056

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
** L  51 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 = 0.3898 r_free = 0.3898 target = 0.166060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.133136 restraints weight = 5978.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.137363 restraints weight = 3760.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.140216 restraints weight = 2702.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3527  Z= 0.121
  Angle     :  0.699   9.089   4816  Z= 0.341
  Chirality :  0.053   0.307    527
  Planarity :  0.004   0.041    622
  Dihedral  :  6.580  49.398    551
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.24 (0.41), residues: 435
  helix: -4.70 (0.45), residues: 28
  sheet: -1.11 (0.48), residues: 123
  loop : -1.34 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  36 
 HIS   0.002   0.000   HIS L  38 
 PHE   0.011   0.001   PHE H  90 
 TYR   0.017   0.002   TYR H  99 
 ARG   0.001   0.000   ARG L  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00796 (    2)
  link_NAG-ASN         : angle       4.95935 (    6)
  link_BETA1-4         : bond        0.00474 (    1)
  link_BETA1-4         : angle       2.23327 (    3)
  hydrogen bonds       : bond        0.03193 (   91)
  hydrogen bonds       : angle       5.75710 (  222)
  SS BOND              : bond        0.00139 (    6)
  SS BOND              : angle       0.64906 (   12)
  covalent geometry    : bond        0.00293 ( 3518)
  covalent geometry    : angle       0.67466 ( 4795)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8934 (m100) cc_final: 0.8536 (m100)
REVERT: H   54 LEU cc_start: 0.8808 (mp) cc_final: 0.7904 (tt)
REVERT: H   83 ARG cc_start: 0.7402 (mtm110) cc_final: 0.6769 (mtm110)
REVERT: H   86 ASP cc_start: 0.7715 (m-30) cc_final: 0.7023 (m-30)
REVERT: H  112 ASP cc_start: 0.9114 (t70) cc_final: 0.8898 (t0)
REVERT: L   47 LEU cc_start: 0.8867 (mt) cc_final: 0.8478 (mt)
REVERT: L   61 ARG cc_start: 0.8270 (mtp180) cc_final: 0.8021 (mtp180)
REVERT: L   95 VAL cc_start: 0.8434 (m) cc_final: 0.8175 (p)
REVERT: T  396 TYR cc_start: 0.8575 (m-80) cc_final: 0.8242 (m-80)
REVERT: T  418 ILE cc_start: 0.9381 (tp) cc_final: 0.9175 (tt)
REVERT: T  449 TYR cc_start: 0.9179 (m-80) cc_final: 0.8963 (m-80)
REVERT: T  467 ASP cc_start: 0.7323 (t0) cc_final: 0.6693 (m-30)
REVERT: T  515 PHE cc_start: 0.8751 (m-80) cc_final: 0.8357 (m-10)
REVERT: T  516 GLU cc_start: 0.6775 (tp30) cc_final: 0.6546 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1606
  time to fit residues: 23.0805
Evaluate side-chains
  101 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0010
   chunk 20 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.5994

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 474 GLN ** 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 = 0.3825 r_free = 0.3825 target = 0.159499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.125466 restraints weight = 6088.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.129520 restraints weight = 3924.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.132315 restraints weight = 2865.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   3527  Z= 0.280
  Angle     :  0.821   8.991   4816  Z= 0.404
  Chirality :  0.059   0.305    527
  Planarity :  0.005   0.046    622
  Dihedral  :  7.164  46.742    551
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.49 %
    Favored  : 88.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.39 (0.41), residues: 435
  helix: -4.66 (0.51), residues: 22
  sheet: -1.16 (0.47), residues: 119
  loop : -1.58 (0.39), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H  47 
 HIS   0.003   0.001   HIS L  38 
 PHE   0.027   0.003   PHE T 371 
 TYR   0.039   0.003   TYR T 421 
 ARG   0.002   0.000   ARG L  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00445 (    2)
  link_NAG-ASN         : angle       4.82740 (    6)
  link_BETA1-4         : bond        0.00422 (    1)
  link_BETA1-4         : angle       2.47181 (    3)
  hydrogen bonds       : bond        0.03898 (   91)
  hydrogen bonds       : angle       6.10259 (  222)
  SS BOND              : bond        0.00310 (    6)
  SS BOND              : angle       0.76113 (   12)
  covalent geometry    : bond        0.00663 ( 3518)
  covalent geometry    : angle       0.80179 ( 4795)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: H   83 ARG cc_start: 0.7454 (mtm110) cc_final: 0.6784 (mtm110)
REVERT: H   86 ASP cc_start: 0.7753 (m-30) cc_final: 0.6991 (m-30)
REVERT: H  112 ASP cc_start: 0.9198 (t70) cc_final: 0.8976 (t0)
REVERT: L   37 GLN cc_start: 0.6828 (tt0) cc_final: 0.6622 (tt0)
REVERT: L   61 ARG cc_start: 0.8305 (mtp180) cc_final: 0.7642 (mtp180)
REVERT: L   76 THR cc_start: 0.8788 (t) cc_final: 0.8502 (t)
REVERT: L  104 LEU cc_start: 0.8219 (tp) cc_final: 0.7893 (tt)
REVERT: T  396 TYR cc_start: 0.8740 (m-80) cc_final: 0.8359 (m-80)
REVERT: T  516 GLU cc_start: 0.6948 (tp30) cc_final: 0.6679 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1535
  time to fit residues: 21.0051
Evaluate side-chains
  96 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 38 optimal weight:    0.1980
   chunk 28 optimal weight:    0.4980
   chunk 39 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 8 optimal weight:    5.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  51 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 = 0.3886 r_free = 0.3886 target = 0.164728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131507 restraints weight = 5847.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.135690 restraints weight = 3701.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.138557 restraints weight = 2678.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   3527  Z= 0.142
  Angle     :  0.730   8.900   4816  Z= 0.357
  Chirality :  0.054   0.311    527
  Planarity :  0.004   0.036    622
  Dihedral  :  6.857  48.168    551
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  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: -2.38 (0.41), residues: 435
  helix: -4.74 (0.43), residues: 28
  sheet: -1.27 (0.45), residues: 131
  loop : -1.39 (0.41), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  36 
 HIS   0.002   0.001   HIS L  38 
 PHE   0.013   0.002   PHE H  90 
 TYR   0.022   0.002   TYR T 453 
 ARG   0.002   0.000   ARG L  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00622 (    2)
  link_NAG-ASN         : angle       4.87565 (    6)
  link_BETA1-4         : bond        0.00420 (    1)
  link_BETA1-4         : angle       2.27110 (    3)
  hydrogen bonds       : bond        0.03328 (   91)
  hydrogen bonds       : angle       6.04538 (  222)
  SS BOND              : bond        0.00197 (    6)
  SS BOND              : angle       0.66165 (   12)
  covalent geometry    : bond        0.00352 ( 3518)
  covalent geometry    : angle       0.70752 ( 4795)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: H   35 ILE cc_start: 0.8602 (mt) cc_final: 0.7661 (mt)
REVERT: H   36 TRP cc_start: 0.8938 (m100) cc_final: 0.8547 (m100)
REVERT: H   83 ARG cc_start: 0.7427 (mtm110) cc_final: 0.6757 (mtm110)
REVERT: H   86 ASP cc_start: 0.7625 (m-30) cc_final: 0.6911 (m-30)
REVERT: H  112 ASP cc_start: 0.9148 (t70) cc_final: 0.8882 (t0)
REVERT: L   47 LEU cc_start: 0.8847 (mt) cc_final: 0.8481 (mt)
REVERT: L   61 ARG cc_start: 0.8317 (mtp180) cc_final: 0.8036 (mtp180)
REVERT: T  396 TYR cc_start: 0.8612 (m-80) cc_final: 0.8274 (m-80)
REVERT: T  516 GLU cc_start: 0.6831 (tp30) cc_final: 0.6588 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1505
  time to fit residues: 21.1235
Evaluate side-chains
  104 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    0.3980
   chunk 8 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0770
   chunk 22 optimal weight:    3.9990
   chunk 23 optimal weight:    0.1980
   chunk 34 optimal weight:    0.0070
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0870
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.1534

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
T 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.168770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.135658 restraints weight = 5900.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.139973 restraints weight = 3717.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.142952 restraints weight = 2665.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3527  Z= 0.121
  Angle     :  0.724   9.146   4816  Z= 0.358
  Chirality :  0.054   0.314    527
  Planarity :  0.005   0.036    622
  Dihedral  :  6.662  50.478    551
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.28 (0.41), residues: 435
  helix: -4.69 (0.46), residues: 28
  sheet: -1.17 (0.46), residues: 131
  loop : -1.34 (0.40), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  36 
 HIS   0.001   0.001   HIS L  38 
 PHE   0.010   0.001   PHE T 371 
 TYR   0.021   0.002   TYR T 453 
 ARG   0.007   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00823 (    2)
  link_NAG-ASN         : angle       4.88100 (    6)
  link_BETA1-4         : bond        0.00587 (    1)
  link_BETA1-4         : angle       2.31745 (    3)
  hydrogen bonds       : bond        0.03223 (   91)
  hydrogen bonds       : angle       5.74672 (  222)
  SS BOND              : bond        0.00147 (    6)
  SS BOND              : angle       0.62302 (   12)
  covalent geometry    : bond        0.00286 ( 3518)
  covalent geometry    : angle       0.70116 ( 4795)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8938 (m100) cc_final: 0.8578 (m100)
REVERT: H   69 ILE cc_start: 0.8877 (mt) cc_final: 0.8521 (mt)
REVERT: H   83 ARG cc_start: 0.7431 (mtm110) cc_final: 0.6806 (mtm110)
REVERT: H   86 ASP cc_start: 0.7686 (m-30) cc_final: 0.6891 (m-30)
REVERT: H  112 ASP cc_start: 0.9064 (t70) cc_final: 0.8864 (t0)
REVERT: L   47 LEU cc_start: 0.8802 (mt) cc_final: 0.8304 (mt)
REVERT: L   61 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7572 (mtp180)
REVERT: L   76 THR cc_start: 0.8613 (t) cc_final: 0.8320 (t)
REVERT: T  396 TYR cc_start: 0.8560 (m-80) cc_final: 0.8233 (m-80)
REVERT: T  449 TYR cc_start: 0.9145 (m-80) cc_final: 0.8942 (m-80)
REVERT: T  467 ASP cc_start: 0.7278 (t0) cc_final: 0.6279 (m-30)
REVERT: T  515 PHE cc_start: 0.8620 (m-80) cc_final: 0.8276 (m-10)
REVERT: T  516 GLU cc_start: 0.6690 (tp30) cc_final: 0.6386 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1627
  time to fit residues: 22.5265
Evaluate side-chains
  104 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 3 optimal weight:    0.4980
   chunk 11 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0040
   chunk 39 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.4792

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.168169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.134848 restraints weight = 5987.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.139136 restraints weight = 3789.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.142131 restraints weight = 2728.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3527  Z= 0.134
  Angle     :  0.714   8.758   4816  Z= 0.351
  Chirality :  0.054   0.307    527
  Planarity :  0.004   0.035    622
  Dihedral  :  6.614  50.236    551
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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: -2.11 (0.42), residues: 435
  helix: -4.74 (0.46), residues: 28
  sheet: -1.11 (0.48), residues: 121
  loop : -1.18 (0.40), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  36 
 HIS   0.002   0.001   HIS H  79 
 PHE   0.015   0.002   PHE H  90 
 TYR   0.025   0.002   TYR T 453 
 ARG   0.005   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00750 (    2)
  link_NAG-ASN         : angle       4.73991 (    6)
  link_BETA1-4         : bond        0.00540 (    1)
  link_BETA1-4         : angle       2.38275 (    3)
  hydrogen bonds       : bond        0.03199 (   91)
  hydrogen bonds       : angle       5.83186 (  222)
  SS BOND              : bond        0.00163 (    6)
  SS BOND              : angle       0.60203 (   12)
  covalent geometry    : bond        0.00328 ( 3518)
  covalent geometry    : angle       0.69261 ( 4795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1773.40 seconds
wall clock time: 31 minutes 42.65 seconds (1902.65 seconds total)