Starting phenix.real_space_refine
on Sat Apr 26 21:14:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bll_44666/04_2025/9bll_44666_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bll_44666/04_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_44666/04_2025/9bll_44666.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bll_44666/04_2025/9bll_44666.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bll_44666/04_2025/9bll_44666_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bll_44666/04_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-5669/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: 3.27, per 1000 atoms: 0.95
  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: 0.75
  Conformation dependent library (CDL) restraints added in 357.5 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: 0.52
  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: 0.95

  Time building geometry restraints manager: 0.89 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:             4.300
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.600
  Find NCS groups from input model:        0.040
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.100
-------------------------------------------------------------------------------
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  : 0.387 
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: 0.1595
  time to fit residues: 21.5049
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  : 0.397 
-------------------------------------------------------------------------------
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:    0.9980
   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:    0.7980

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.161391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.128701 restraints weight = 5948.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.132423 restraints weight = 3841.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.135064 restraints weight = 2812.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   3527  Z= 0.168
  Angle     :  0.747   9.445   4816  Z= 0.372
  Chirality :  0.055   0.305    527
  Planarity :  0.005   0.045    622
  Dihedral  :  7.407  49.334    551
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  5.46 %
    Favored  : 93.99 %
  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   0.018   0.002   TRP H  36 
 HIS   0.004   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        0.00735 (    2)
  link_NAG-ASN         : angle       5.07759 (    6)
  link_BETA1-4         : bond        0.00417 (    1)
  link_BETA1-4         : angle       2.13390 (    3)
  hydrogen bonds       : bond        0.03854 (   91)
  hydrogen bonds       : angle       6.53573 (  222)
  SS BOND              : bond        0.00172 (    6)
  SS BOND              : angle       0.90353 (   12)
  covalent geometry    : bond        0.00396 ( 3518)
  covalent geometry    : angle       0.72377 ( 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
  113 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.9043 (m100) cc_final: 0.8735 (m100)
REVERT: H   59 TYR cc_start: 0.8272 (m-80) cc_final: 0.7985 (m-80)
REVERT: H   83 ARG cc_start: 0.7448 (mtm110) cc_final: 0.7136 (mtm110)
REVERT: H   86 ASP cc_start: 0.7682 (m-30) cc_final: 0.7190 (m-30)
REVERT: H  112 ASP cc_start: 0.9179 (t70) cc_final: 0.8951 (t0)
REVERT: L   47 LEU cc_start: 0.8850 (mt) cc_final: 0.8579 (mt)
REVERT: L   95 VAL cc_start: 0.8256 (m) cc_final: 0.7773 (m)
REVERT: T  418 ILE cc_start: 0.9500 (tp) cc_final: 0.9237 (tt)
REVERT: T  516 GLU cc_start: 0.6707 (tp30) cc_final: 0.6397 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1432
  time to fit residues: 19.8642
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  : 0.355 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 0 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0570
   chunk 15 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.5100

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3867 r_free = 0.3867 target = 0.163434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.130239 restraints weight = 5983.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.134360 restraints weight = 3808.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.137200 restraints weight = 2753.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3527  Z= 0.132
  Angle     :  0.700   9.080   4816  Z= 0.347
  Chirality :  0.053   0.299    527
  Planarity :  0.005   0.045    622
  Dihedral  :  7.094  49.655    551
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  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: -2.43 (0.41), residues: 435
  helix: -4.57 (0.47), residues: 22
  sheet: -1.10 (0.48), residues: 122
  loop : -1.67 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP T 436 
 HIS   0.003   0.001   HIS L  34 
 PHE   0.012   0.001   PHE T 429 
 TYR   0.013   0.001   TYR T 489 
 ARG   0.002   0.000   ARG L  27 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00667 (    2)
  link_NAG-ASN         : angle       4.93059 (    6)
  link_BETA1-4         : bond        0.00443 (    1)
  link_BETA1-4         : angle       2.13132 (    3)
  hydrogen bonds       : bond        0.03454 (   91)
  hydrogen bonds       : angle       6.14301 (  222)
  SS BOND              : bond        0.00207 (    6)
  SS BOND              : angle       0.74047 (   12)
  covalent geometry    : bond        0.00308 ( 3518)
  covalent geometry    : angle       0.67614 ( 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  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: H   86 ASP cc_start: 0.7665 (m-30) cc_final: 0.7026 (m-30)
REVERT: H  112 ASP cc_start: 0.9132 (t70) cc_final: 0.8928 (t0)
REVERT: L   47 LEU cc_start: 0.8875 (mt) cc_final: 0.8505 (mt)
REVERT: L   95 VAL cc_start: 0.8377 (m) cc_final: 0.7952 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1533
  time to fit residues: 21.2397
Evaluate side-chains
  97 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0370
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.6658

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.162818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.129638 restraints weight = 5964.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.133816 restraints weight = 3754.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136669 restraints weight = 2695.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1750

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= 0.146
  Angle     :  0.702   9.057   4816  Z= 0.346
  Chirality :  0.053   0.310    527
  Planarity :  0.005   0.044    622
  Dihedral  :  6.892  48.922    551
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  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: -4.52 (0.51), residues: 22
  sheet: -1.13 (0.47), residues: 126
  loop : -1.61 (0.39), residues: 287

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   0.002   PHE T 429 
 TYR   0.012   0.001   TYR H 106 
 ARG   0.003   0.000   ARG H  83 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00636 (    2)
  link_NAG-ASN         : angle       4.96743 (    6)
  link_BETA1-4         : bond        0.00378 (    1)
  link_BETA1-4         : angle       2.09372 (    3)
  hydrogen bonds       : bond        0.03484 (   91)
  hydrogen bonds       : angle       6.09624 (  222)
  SS BOND              : bond        0.00424 (    6)
  SS BOND              : angle       0.62630 (   12)
  covalent geometry    : bond        0.00353 ( 3518)
  covalent geometry    : angle       0.67833 ( 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
  110 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: H   69 ILE cc_start: 0.9003 (mt) cc_final: 0.8752 (mt)
REVERT: H   86 ASP cc_start: 0.7672 (m-30) cc_final: 0.7263 (m-30)
REVERT: L   33 VAL cc_start: 0.7017 (m) cc_final: 0.6722 (m)
REVERT: L   47 LEU cc_start: 0.8891 (mt) cc_final: 0.8484 (mt)
REVERT: L   95 VAL cc_start: 0.8285 (m) cc_final: 0.7889 (m)
REVERT: T  516 GLU cc_start: 0.6874 (tp30) cc_final: 0.6617 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1484
  time to fit residues: 19.9834
Evaluate side-chains
  100 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 5 optimal weight:    0.0770
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0980
   chunk 37 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.4338

-------------------------------------------------------------------------------
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 474 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 = 0.3894 r_free = 0.3894 target = 0.165762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.132609 restraints weight = 5965.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.136814 restraints weight = 3760.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.139713 restraints weight = 2686.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2092

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= 0.126
  Angle     :  0.698   9.108   4816  Z= 0.342
  Chirality :  0.053   0.307    527
  Planarity :  0.005   0.043    622
  Dihedral  :  6.700  49.281    551
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  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: -2.25 (0.41), residues: 435
  helix: -4.67 (0.43), residues: 28
  sheet: -0.96 (0.47), residues: 125
  loop : -1.44 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  36 
 HIS   0.002   0.001   HIS L  38 
 PHE   0.010   0.001   PHE T 429 
 TYR   0.012   0.002   TYR H 106 
 ARG   0.002   0.000   ARG H  83 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00741 (    2)
  link_NAG-ASN         : angle       4.96573 (    6)
  link_BETA1-4         : bond        0.00369 (    1)
  link_BETA1-4         : angle       2.13047 (    3)
  hydrogen bonds       : bond        0.03285 (   91)
  hydrogen bonds       : angle       5.83066 (  222)
  SS BOND              : bond        0.00104 (    6)
  SS BOND              : angle       0.61524 (   12)
  covalent geometry    : bond        0.00302 ( 3518)
  covalent geometry    : angle       0.67466 ( 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
  107 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.9022 (m100) cc_final: 0.8585 (m100)
REVERT: H   83 ARG cc_start: 0.7452 (mtm110) cc_final: 0.6581 (mtm110)
REVERT: H   86 ASP cc_start: 0.7670 (m-30) cc_final: 0.7089 (m-30)
REVERT: L   33 VAL cc_start: 0.7033 (m) cc_final: 0.6782 (m)
REVERT: L   47 LEU cc_start: 0.8872 (mt) cc_final: 0.8437 (mt)
REVERT: L   95 VAL cc_start: 0.8460 (m) cc_final: 0.8070 (m)
REVERT: T  516 GLU cc_start: 0.6825 (tp30) cc_final: 0.6538 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1550
  time to fit residues: 20.3131
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  : 0.414 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0050
   overall best weight:    1.5200

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.158815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.125140 restraints weight = 6099.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.129272 restraints weight = 3842.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.132087 restraints weight = 2746.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   3527  Z= 0.265
  Angle     :  0.791   8.787   4816  Z= 0.392
  Chirality :  0.058   0.307    527
  Planarity :  0.005   0.047    622
  Dihedral  :  7.112  46.808    551
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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: -2.42 (0.41), residues: 435
  helix: -4.54 (0.50), residues: 22
  sheet: -1.35 (0.45), residues: 134
  loop : -1.51 (0.40), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP T 436 
 HIS   0.003   0.001   HIS L  38 
 PHE   0.018   0.003   PHE T 371 
 TYR   0.027   0.003   TYR T 421 
 ARG   0.004   0.000   ARG L  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00469 (    2)
  link_NAG-ASN         : angle       4.84836 (    6)
  link_BETA1-4         : bond        0.00413 (    1)
  link_BETA1-4         : angle       2.42486 (    3)
  hydrogen bonds       : bond        0.04010 (   91)
  hydrogen bonds       : angle       6.15695 (  222)
  SS BOND              : bond        0.00281 (    6)
  SS BOND              : angle       0.69058 (   12)
  covalent geometry    : bond        0.00625 ( 3518)
  covalent geometry    : angle       0.77065 ( 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
  110 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: H   83 ARG cc_start: 0.7257 (mtm110) cc_final: 0.6512 (mtm110)
REVERT: H   86 ASP cc_start: 0.7724 (m-30) cc_final: 0.7073 (m-30)
REVERT: H  112 ASP cc_start: 0.9181 (t70) cc_final: 0.8961 (t0)
REVERT: L   33 VAL cc_start: 0.7298 (m) cc_final: 0.7088 (m)
REVERT: L   47 LEU cc_start: 0.8937 (mt) cc_final: 0.8603 (mt)
REVERT: L   95 VAL cc_start: 0.8454 (m) cc_final: 0.8247 (m)
REVERT: L  104 LEU cc_start: 0.8197 (tp) cc_final: 0.7853 (tt)
REVERT: T  516 GLU cc_start: 0.7023 (tp30) cc_final: 0.6717 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1516
  time to fit residues: 20.3278
Evaluate side-chains
  95 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0020
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.163817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.130692 restraints weight = 5969.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.134941 restraints weight = 3707.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.137752 restraints weight = 2647.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2119

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= 0.138
  Angle     :  0.714   8.962   4816  Z= 0.348
  Chirality :  0.054   0.305    527
  Planarity :  0.004   0.041    622
  Dihedral  :  6.804  48.120    551
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.09 %
    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: -2.32 (0.42), residues: 435
  helix: -4.73 (0.44), residues: 28
  sheet: -1.21 (0.45), residues: 133
  loop : -1.36 (0.41), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  36 
 HIS   0.002   0.001   HIS L  38 
 PHE   0.011   0.001   PHE T 392 
 TYR   0.016   0.002   TYR H 106 
 ARG   0.002   0.000   ARG L  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00676 (    2)
  link_NAG-ASN         : angle       4.97351 (    6)
  link_BETA1-4         : bond        0.00384 (    1)
  link_BETA1-4         : angle       2.22478 (    3)
  hydrogen bonds       : bond        0.03291 (   91)
  hydrogen bonds       : angle       5.96277 (  222)
  SS BOND              : bond        0.00149 (    6)
  SS BOND              : angle       0.63963 (   12)
  covalent geometry    : bond        0.00335 ( 3518)
  covalent geometry    : angle       0.69081 ( 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
  113 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.336 
Fit side-chains
REVERT: H   83 ARG cc_start: 0.7402 (mtm110) cc_final: 0.6705 (mtm110)
REVERT: H   86 ASP cc_start: 0.7636 (m-30) cc_final: 0.6947 (m-30)
REVERT: H  112 ASP cc_start: 0.9162 (t70) cc_final: 0.8921 (t0)
REVERT: L    6 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6420 (pm20)
REVERT: L   33 VAL cc_start: 0.7116 (m) cc_final: 0.6891 (m)
REVERT: L   47 LEU cc_start: 0.8894 (mt) cc_final: 0.8453 (mt)
REVERT: L   61 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7625 (mtp180)
REVERT: L   76 THR cc_start: 0.8672 (t) cc_final: 0.8425 (t)
REVERT: L   95 VAL cc_start: 0.8590 (m) cc_final: 0.8209 (m)
REVERT: T  467 ASP cc_start: 0.7237 (t0) cc_final: 0.6344 (m-30)
REVERT: T  516 GLU cc_start: 0.6924 (tp30) cc_final: 0.6602 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1566
  time to fit residues: 21.4117
Evaluate side-chains
  103 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0980
   chunk 13 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0670
   chunk 16 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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
** L  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.164525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131350 restraints weight = 6024.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.135569 restraints weight = 3744.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.138473 restraints weight = 2674.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   3527  Z= 0.137
  Angle     :  0.711   8.965   4816  Z= 0.347
  Chirality :  0.054   0.303    527
  Planarity :  0.004   0.040    622
  Dihedral  :  6.672  49.122    551
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.15
  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: -2.30 (0.42), residues: 435
  helix: -4.72 (0.44), residues: 28
  sheet: -1.24 (0.45), residues: 135
  loop : -1.32 (0.41), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  36 
 HIS   0.002   0.001   HIS L  38 
 PHE   0.011   0.002   PHE H  90 
 TYR   0.024   0.002   TYR T 421 
 ARG   0.001   0.000   ARG T 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00702 (    2)
  link_NAG-ASN         : angle       4.91477 (    6)
  link_BETA1-4         : bond        0.00443 (    1)
  link_BETA1-4         : angle       2.29457 (    3)
  hydrogen bonds       : bond        0.03294 (   91)
  hydrogen bonds       : angle       5.87218 (  222)
  SS BOND              : bond        0.00171 (    6)
  SS BOND              : angle       0.68677 (   12)
  covalent geometry    : bond        0.00337 ( 3518)
  covalent geometry    : angle       0.68821 ( 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
  114 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8905 (m100) cc_final: 0.8507 (m100)
REVERT: H   69 ILE cc_start: 0.8900 (mt) cc_final: 0.8602 (mt)
REVERT: H   83 ARG cc_start: 0.7378 (mtm110) cc_final: 0.6682 (mtm110)
REVERT: H   86 ASP cc_start: 0.7639 (m-30) cc_final: 0.6904 (m-30)
REVERT: H  112 ASP cc_start: 0.9146 (t70) cc_final: 0.8927 (t0)
REVERT: L   47 LEU cc_start: 0.8883 (mt) cc_final: 0.8469 (mt)
REVERT: L   61 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7602 (mtp180)
REVERT: L   76 THR cc_start: 0.8635 (t) cc_final: 0.8379 (t)
REVERT: L   95 VAL cc_start: 0.8463 (m) cc_final: 0.8222 (p)
REVERT: T  467 ASP cc_start: 0.7151 (t0) cc_final: 0.6315 (m-30)
REVERT: T  516 GLU cc_start: 0.6909 (tp30) cc_final: 0.6594 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1616
  time to fit residues: 22.0475
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  : 0.350 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 38 optimal weight:    0.0670
   chunk 28 optimal weight:    0.0070
   chunk 39 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0980
   chunk 32 optimal weight:    0.3980
   chunk 34 optimal weight:    0.2980
   chunk 27 optimal weight:    0.1980
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.0874

-------------------------------------------------------------------------------
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 = 0.3937 r_free = 0.3937 target = 0.169288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.136608 restraints weight = 5830.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.141032 restraints weight = 3602.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.143963 restraints weight = 2556.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2642

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= 0.120
  Angle     :  0.706   9.318   4816  Z= 0.347
  Chirality :  0.053   0.305    527
  Planarity :  0.004   0.038    622
  Dihedral  :  6.530  50.756    551
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  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: -2.11 (0.42), residues: 435
  helix: -4.71 (0.45), residues: 28
  sheet: -0.98 (0.47), residues: 129
  loop : -1.25 (0.41), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  36 
 HIS   0.002   0.001   HIS T 505 
 PHE   0.021   0.001   PHE T 429 
 TYR   0.011   0.001   TYR H 106 
 ARG   0.002   0.000   ARG H 102 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00902 (    2)
  link_NAG-ASN         : angle       4.99481 (    6)
  link_BETA1-4         : bond        0.00467 (    1)
  link_BETA1-4         : angle       2.30171 (    3)
  hydrogen bonds       : bond        0.03160 (   91)
  hydrogen bonds       : angle       5.78889 (  222)
  SS BOND              : bond        0.00168 (    6)
  SS BOND              : angle       0.68287 (   12)
  covalent geometry    : bond        0.00281 ( 3518)
  covalent geometry    : angle       0.68222 ( 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
  109 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8949 (m100) cc_final: 0.8578 (m100)
REVERT: H   69 ILE cc_start: 0.8929 (mt) cc_final: 0.8671 (mt)
REVERT: H   83 ARG cc_start: 0.7352 (mtm110) cc_final: 0.6713 (mtm110)
REVERT: H   86 ASP cc_start: 0.7600 (m-30) cc_final: 0.6921 (m-30)
REVERT: H  112 ASP cc_start: 0.9111 (t70) cc_final: 0.8851 (t0)
REVERT: L   47 LEU cc_start: 0.8847 (mt) cc_final: 0.8403 (mt)
REVERT: L   61 ARG cc_start: 0.8269 (mtp180) cc_final: 0.7588 (mtp180)
REVERT: L   76 THR cc_start: 0.8571 (t) cc_final: 0.8321 (t)
REVERT: T  467 ASP cc_start: 0.6853 (t0) cc_final: 0.6099 (m-30)
REVERT: T  516 GLU cc_start: 0.6794 (tp30) cc_final: 0.6576 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1467
  time to fit residues: 19.6230
Evaluate side-chains
  100 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0370
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7262

-------------------------------------------------------------------------------
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 = 0.3897 r_free = 0.3897 target = 0.165636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.132453 restraints weight = 5997.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.136544 restraints weight = 3791.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.139379 restraints weight = 2731.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   3527  Z= 0.158
  Angle     :  0.726   8.818   4816  Z= 0.355
  Chirality :  0.054   0.300    527
  Planarity :  0.004   0.040    622
  Dihedral  :  6.625  49.686    551
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.42), residues: 435
  helix: -4.80 (0.42), residues: 28
  sheet: -1.00 (0.47), residues: 132
  loop : -1.28 (0.41), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  36 
 HIS   0.002   0.001   HIS L  38 
 PHE   0.024   0.002   PHE T 429 
 TYR   0.021   0.002   TYR H 106 
 ARG   0.002   0.000   ARG L  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00712 (    2)
  link_NAG-ASN         : angle       4.81504 (    6)
  link_BETA1-4         : bond        0.00540 (    1)
  link_BETA1-4         : angle       2.34579 (    3)
  hydrogen bonds       : bond        0.03325 (   91)
  hydrogen bonds       : angle       5.77489 (  222)
  SS BOND              : bond        0.00190 (    6)
  SS BOND              : angle       0.63774 (   12)
  covalent geometry    : bond        0.00386 ( 3518)
  covalent geometry    : angle       0.70450 ( 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
  108 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8915 (m100) cc_final: 0.8551 (m100)
REVERT: H   83 ARG cc_start: 0.7434 (mtm110) cc_final: 0.7163 (mtm110)
REVERT: H   86 ASP cc_start: 0.7626 (m-30) cc_final: 0.7126 (m-30)
REVERT: H  112 ASP cc_start: 0.9136 (t70) cc_final: 0.8896 (t0)
REVERT: L   47 LEU cc_start: 0.8793 (mt) cc_final: 0.8438 (mt)
REVERT: L   61 ARG cc_start: 0.8297 (mtp180) cc_final: 0.8025 (mtp180)
REVERT: L  104 LEU cc_start: 0.8067 (tp) cc_final: 0.7755 (tt)
REVERT: T  516 GLU cc_start: 0.6829 (tp30) cc_final: 0.6586 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1726
  time to fit residues: 22.2890
Evaluate side-chains
  100 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0170
   chunk 9 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0770
   overall best weight:    0.4176

-------------------------------------------------------------------------------
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 = 0.3909 r_free = 0.3909 target = 0.166898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.133769 restraints weight = 5996.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.138037 restraints weight = 3740.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.140985 restraints weight = 2668.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3527  Z= 0.127
  Angle     :  0.700   8.946   4816  Z= 0.344
  Chirality :  0.054   0.306    527
  Planarity :  0.004   0.038    622
  Dihedral  :  6.521  50.168    551
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.00
  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: -2.17 (0.42), residues: 435
  helix: -4.74 (0.46), residues: 28
  sheet: -1.04 (0.46), residues: 132
  loop : -1.27 (0.41), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  47 
 HIS   0.001   0.001   HIS L  38 
 PHE   0.022   0.002   PHE T 429 
 TYR   0.023   0.002   TYR T 473 
 ARG   0.002   0.000   ARG L  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00719 (    2)
  link_NAG-ASN         : angle       4.79079 (    6)
  link_BETA1-4         : bond        0.00569 (    1)
  link_BETA1-4         : angle       2.34859 (    3)
  hydrogen bonds       : bond        0.03194 (   91)
  hydrogen bonds       : angle       5.66810 (  222)
  SS BOND              : bond        0.00177 (    6)
  SS BOND              : angle       0.60524 (   12)
  covalent geometry    : bond        0.00312 ( 3518)
  covalent geometry    : angle       0.67797 ( 4795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1754.24 seconds
wall clock time: 31 minutes 6.16 seconds (1866.16 seconds total)