Starting phenix.real_space_refine
on Wed Sep 17 03:47:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bll_44666/09_2025/9bll_44666_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bll_44666/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bll_44666/09_2025/9bll_44666_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bll_44666/09_2025/9bll_44666_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bll_44666/09_2025/9bll_44666.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bll_44666/09_2025/9bll_44666.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.20, per 1000 atoms: 0.35
  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: 0.38
  Conformation dependent library (CDL) restraints added in 142.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.11
  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: 0.41

  Time building geometry restraints manager: 0.44 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:             7.250
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.610
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.150
-------------------------------------------------------------------------------
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 : 24.07
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.86 (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
 ARG   0.005   0.001   ARG L  27 
 TYR   0.034   0.003   TYR H 106 
 PHE   0.023   0.003   PHE T 371 
 TRP   0.026   0.003   TRP H  36 
 HIS   0.005   0.002   HIS T 505 

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

*********************** 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  : 0.111 
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: 0.0613
  time to fit residues: 8.2853
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  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0570
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.3862 r_free = 0.3862 target = 0.162551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.129657 restraints weight = 6044.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.133569 restraints weight = 3875.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.136131 restraints weight = 2819.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.138085 restraints weight = 2264.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.139347 restraints weight = 1922.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3527  Z= 0.148
  Angle     :  0.740   9.557   4816  Z= 0.367
  Chirality :  0.055   0.316    527
  Planarity :  0.005   0.045    622
  Dihedral  :  7.402  49.771    551
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.89 %
    Favored  : 90.11 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.57 (0.41), residues: 435
  helix: -4.85 (0.31), residues: 28
  sheet: -1.27 (0.47), residues: 122
  loop : -1.61 (0.39), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  61 
 TYR   0.013   0.002   TYR T 351 
 PHE   0.016   0.002   PHE T 429 
 TRP   0.017   0.002   TRP H  36 
 HIS   0.004   0.001   HIS T 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3518)
  covalent geometry    : angle       0.71543 ( 4795)
  SS BOND              : bond        0.00238 (    6)
  SS BOND              : angle       0.91596 (   12)
  hydrogen bonds       : bond        0.03812 (   91)
  hydrogen bonds       : angle       6.54152 (  222)
  link_BETA1-4         : bond        0.00557 (    1)
  link_BETA1-4         : angle       2.23874 (    3)
  link_NAG-ASN         : bond        0.00672 (    2)
  link_NAG-ASN         : angle       5.08680 (    6)

*********************** 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
  111 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.9022 (m100) cc_final: 0.8720 (m100)
REVERT: H   59 TYR cc_start: 0.8250 (m-80) cc_final: 0.7980 (m-80)
REVERT: H   83 ARG cc_start: 0.7383 (mtm110) cc_final: 0.7104 (mtm110)
REVERT: H   86 ASP cc_start: 0.7797 (m-30) cc_final: 0.7340 (m-30)
REVERT: H  111 MET cc_start: 0.8723 (mpp) cc_final: 0.8369 (mpp)
REVERT: H  112 ASP cc_start: 0.9187 (t70) cc_final: 0.8935 (t0)
REVERT: L   47 LEU cc_start: 0.8817 (mt) cc_final: 0.8551 (mt)
REVERT: L   95 VAL cc_start: 0.8308 (m) cc_final: 0.7809 (m)
REVERT: T  396 TYR cc_start: 0.8510 (m-80) cc_final: 0.8302 (m-80)
REVERT: T  516 GLU cc_start: 0.6673 (tp30) cc_final: 0.6366 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0579
  time to fit residues: 7.9301
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  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 5 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.160788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.127351 restraints weight = 6061.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.131452 restraints weight = 3858.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.134253 restraints weight = 2781.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.136166 restraints weight = 2212.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.137117 restraints weight = 1888.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3527  Z= 0.183
  Angle     :  0.734   8.773   4816  Z= 0.364
  Chirality :  0.054   0.295    527
  Planarity :  0.005   0.046    622
  Dihedral  :  7.223  48.661    551
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.54 (0.41), residues: 435
  helix: -4.65 (0.46), residues: 22
  sheet: -1.27 (0.47), residues: 127
  loop : -1.69 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  27 
 TYR   0.016   0.002   TYR H 106 
 PHE   0.015   0.002   PHE T 429 
 TRP   0.013   0.002   TRP T 436 
 HIS   0.003   0.001   HIS T 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 3518)
  covalent geometry    : angle       0.71236 ( 4795)
  SS BOND              : bond        0.00430 (    6)
  SS BOND              : angle       0.75724 (   12)
  hydrogen bonds       : bond        0.03739 (   91)
  hydrogen bonds       : angle       6.18691 (  222)
  link_BETA1-4         : bond        0.00312 (    1)
  link_BETA1-4         : angle       2.15772 (    3)
  link_NAG-ASN         : bond        0.00500 (    2)
  link_NAG-ASN         : angle       4.87907 (    6)

*********************** 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
  108 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: H   69 ILE cc_start: 0.9054 (mt) cc_final: 0.8810 (mt)
REVERT: H   86 ASP cc_start: 0.7737 (m-30) cc_final: 0.7260 (m-30)
REVERT: H  112 ASP cc_start: 0.9134 (t70) cc_final: 0.8925 (t0)
REVERT: L   47 LEU cc_start: 0.8910 (mt) cc_final: 0.8553 (mt)
REVERT: L   95 VAL cc_start: 0.8403 (m) cc_final: 0.7989 (m)
REVERT: T  396 TYR cc_start: 0.8571 (m-80) cc_final: 0.8287 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0561
  time to fit residues: 7.5084
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  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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

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 = 0.162037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.128431 restraints weight = 6006.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.132560 restraints weight = 3805.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.135338 restraints weight = 2745.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.137252 restraints weight = 2189.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.138110 restraints weight = 1866.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3527  Z= 0.168
  Angle     :  0.733   8.847   4816  Z= 0.360
  Chirality :  0.055   0.312    527
  Planarity :  0.005   0.044    622
  Dihedral  :  7.006  47.929    551
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.50 (0.41), residues: 435
  helix: -4.61 (0.50), residues: 22
  sheet: -1.30 (0.46), residues: 127
  loop : -1.63 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  83 
 TYR   0.018   0.002   TYR H 106 
 PHE   0.014   0.002   PHE T 429 
 TRP   0.012   0.001   TRP T 436 
 HIS   0.002   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 3518)
  covalent geometry    : angle       0.71048 ( 4795)
  SS BOND              : bond        0.00154 (    6)
  SS BOND              : angle       0.74627 (   12)
  hydrogen bonds       : bond        0.03636 (   91)
  hydrogen bonds       : angle       6.05949 (  222)
  link_BETA1-4         : bond        0.00291 (    1)
  link_BETA1-4         : angle       2.14665 (    3)
  link_NAG-ASN         : bond        0.00513 (    2)
  link_NAG-ASN         : angle       4.92178 (    6)

*********************** 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
  109 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   59 TYR cc_start: 0.8129 (m-80) cc_final: 0.7915 (m-80)
REVERT: H   83 ARG cc_start: 0.7504 (mtm110) cc_final: 0.7295 (mtm110)
REVERT: H   86 ASP cc_start: 0.7754 (m-30) cc_final: 0.7256 (m-30)
REVERT: H  112 ASP cc_start: 0.9133 (t70) cc_final: 0.8886 (t0)
REVERT: L   47 LEU cc_start: 0.8902 (mt) cc_final: 0.8456 (mt)
REVERT: L   95 VAL cc_start: 0.8339 (m) cc_final: 0.7938 (m)
REVERT: T  396 TYR cc_start: 0.8598 (m-80) cc_final: 0.8300 (m-80)
REVERT: T  449 TYR cc_start: 0.9260 (m-80) cc_final: 0.9045 (m-80)
REVERT: T  467 ASP cc_start: 0.7408 (t0) cc_final: 0.6796 (m-30)
REVERT: T  516 GLU cc_start: 0.6943 (tp30) cc_final: 0.6695 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0612
  time to fit residues: 8.3071
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  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 18 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 2 optimal weight:    0.1980
   chunk 26 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 0 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.163881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.130669 restraints weight = 5973.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.134866 restraints weight = 3758.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.137722 restraints weight = 2687.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.139388 restraints weight = 2121.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.140804 restraints weight = 1814.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1971

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= 0.133
  Angle     :  0.710   8.933   4816  Z= 0.348
  Chirality :  0.054   0.305    527
  Planarity :  0.005   0.043    622
  Dihedral  :  6.879  48.718    551
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.19 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.38 (0.41), residues: 435
  helix: -4.54 (0.53), residues: 22
  sheet: -1.22 (0.47), residues: 121
  loop : -1.54 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  93 
 TYR   0.028   0.002   TYR T 501 
 PHE   0.012   0.001   PHE T 429 
 TRP   0.010   0.001   TRP T 436 
 HIS   0.002   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3518)
  covalent geometry    : angle       0.68769 ( 4795)
  SS BOND              : bond        0.00117 (    6)
  SS BOND              : angle       0.61785 (   12)
  hydrogen bonds       : bond        0.03344 (   91)
  hydrogen bonds       : angle       5.90013 (  222)
  link_BETA1-4         : bond        0.00430 (    1)
  link_BETA1-4         : angle       2.26493 (    3)
  link_NAG-ASN         : bond        0.00651 (    2)
  link_NAG-ASN         : angle       4.84493 (    6)

*********************** 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
  116 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: H   69 ILE cc_start: 0.9028 (mt) cc_final: 0.8796 (mt)
REVERT: H   83 ARG cc_start: 0.7489 (mtm110) cc_final: 0.6799 (mtm110)
REVERT: H   86 ASP cc_start: 0.7824 (m-30) cc_final: 0.7035 (m-30)
REVERT: H  112 ASP cc_start: 0.9135 (t70) cc_final: 0.8915 (t0)
REVERT: L    6 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6368 (pm20)
REVERT: L   33 VAL cc_start: 0.7060 (m) cc_final: 0.6786 (m)
REVERT: L   47 LEU cc_start: 0.8891 (mt) cc_final: 0.8416 (mt)
REVERT: L   95 VAL cc_start: 0.8434 (m) cc_final: 0.8037 (m)
REVERT: T  396 TYR cc_start: 0.8580 (m-80) cc_final: 0.8238 (m-80)
REVERT: T  467 ASP cc_start: 0.7338 (t0) cc_final: 0.6761 (m-30)
REVERT: T  516 GLU cc_start: 0.6836 (tp30) cc_final: 0.6578 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0628
  time to fit residues: 8.8711
Evaluate side-chains
  104 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0770
   chunk 18 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0170
   chunk 30 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.4376

-------------------------------------------------------------------------------
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**
T 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.165687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.132814 restraints weight = 5957.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.136944 restraints weight = 3759.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.139800 restraints weight = 2701.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.141792 restraints weight = 2134.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.142853 restraints weight = 1802.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   3527  Z= 0.127
  Angle     :  0.709   9.192   4816  Z= 0.348
  Chirality :  0.054   0.310    527
  Planarity :  0.004   0.042    622
  Dihedral  :  6.728  49.268    551
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.27 (0.41), residues: 435
  helix: -4.56 (0.55), residues: 22
  sheet: -1.03 (0.48), residues: 119
  loop : -1.52 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  66 
 TYR   0.020   0.002   TYR H  59 
 PHE   0.010   0.001   PHE T 429 
 TRP   0.012   0.001   TRP H  36 
 HIS   0.002   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3518)
  covalent geometry    : angle       0.68501 ( 4795)
  SS BOND              : bond        0.00127 (    6)
  SS BOND              : angle       0.64159 (   12)
  hydrogen bonds       : bond        0.03263 (   91)
  hydrogen bonds       : angle       5.81210 (  222)
  link_BETA1-4         : bond        0.00402 (    1)
  link_BETA1-4         : angle       2.16473 (    3)
  link_NAG-ASN         : bond        0.00775 (    2)
  link_NAG-ASN         : angle       5.05797 (    6)

*********************** 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  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8961 (m100) cc_final: 0.8563 (m100)
REVERT: H   83 ARG cc_start: 0.7468 (mtm110) cc_final: 0.6778 (mtm110)
REVERT: H   86 ASP cc_start: 0.7778 (m-30) cc_final: 0.7008 (m-30)
REVERT: H  112 ASP cc_start: 0.9109 (t70) cc_final: 0.8882 (t0)
REVERT: L   33 VAL cc_start: 0.7096 (m) cc_final: 0.6852 (m)
REVERT: L   47 LEU cc_start: 0.8880 (mt) cc_final: 0.8458 (mt)
REVERT: L   61 ARG cc_start: 0.8297 (mtp180) cc_final: 0.7868 (mtp180)
REVERT: L   95 VAL cc_start: 0.8339 (m) cc_final: 0.8007 (m)
REVERT: T  396 TYR cc_start: 0.8558 (m-80) cc_final: 0.8298 (m-80)
REVERT: T  467 ASP cc_start: 0.7203 (t0) cc_final: 0.6641 (m-30)
REVERT: T  515 PHE cc_start: 0.8725 (m-80) cc_final: 0.8351 (m-10)
REVERT: T  516 GLU cc_start: 0.6822 (tp30) cc_final: 0.6523 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0759
  time to fit residues: 10.1423
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  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0050
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.4794

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.166089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.132730 restraints weight = 6073.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.136977 restraints weight = 3823.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.139896 restraints weight = 2749.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.141906 restraints weight = 2171.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.143141 restraints weight = 1834.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3527  Z= 0.128
  Angle     :  0.693   8.907   4816  Z= 0.341
  Chirality :  0.053   0.300    527
  Planarity :  0.004   0.040    622
  Dihedral  :  6.649  49.699    551
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.16 (0.41), residues: 435
  helix: -4.77 (0.43), residues: 28
  sheet: -0.89 (0.49), residues: 115
  loop : -1.35 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG T 403 
 TYR   0.014   0.002   TYR T 453 
 PHE   0.010   0.001   PHE T 429 
 TRP   0.011   0.001   TRP H  36 
 HIS   0.002   0.000   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3518)
  covalent geometry    : angle       0.66958 ( 4795)
  SS BOND              : bond        0.00167 (    6)
  SS BOND              : angle       0.65567 (   12)
  hydrogen bonds       : bond        0.03247 (   91)
  hydrogen bonds       : angle       5.65985 (  222)
  link_BETA1-4         : bond        0.00487 (    1)
  link_BETA1-4         : angle       2.31137 (    3)
  link_NAG-ASN         : bond        0.00659 (    2)
  link_NAG-ASN         : angle       4.81047 (    6)

*********************** 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
  110 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: H   69 ILE cc_start: 0.8904 (mt) cc_final: 0.8685 (mt)
REVERT: H   83 ARG cc_start: 0.7308 (mtm110) cc_final: 0.6746 (mtm110)
REVERT: H   86 ASP cc_start: 0.7801 (m-30) cc_final: 0.6994 (m-30)
REVERT: L   47 LEU cc_start: 0.8875 (mt) cc_final: 0.8489 (mt)
REVERT: L   61 ARG cc_start: 0.8265 (mtp180) cc_final: 0.7602 (mtp180)
REVERT: L   76 THR cc_start: 0.8559 (t) cc_final: 0.8315 (t)
REVERT: L   95 VAL cc_start: 0.8335 (m) cc_final: 0.8089 (m)
REVERT: T  396 TYR cc_start: 0.8532 (m-80) cc_final: 0.8232 (m-80)
REVERT: T  467 ASP cc_start: 0.7160 (t0) cc_final: 0.6540 (m-30)
REVERT: T  473 TYR cc_start: 0.8257 (t80) cc_final: 0.7680 (t80)
REVERT: T  516 GLU cc_start: 0.6784 (tp30) cc_final: 0.6510 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0719
  time to fit residues: 9.6508
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  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 40 optimal weight:    0.3980
   chunk 9 optimal weight:    0.5980
   chunk 16 optimal weight:    0.3980
   chunk 29 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0070
   overall best weight:    0.3398

-------------------------------------------------------------------------------
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 = 0.3924 r_free = 0.3924 target = 0.168043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.134625 restraints weight = 5973.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.138829 restraints weight = 3769.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.141817 restraints weight = 2703.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.143896 restraints weight = 2121.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.144892 restraints weight = 1784.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3527  Z= 0.120
  Angle     :  0.694   9.068   4816  Z= 0.340
  Chirality :  0.053   0.311    527
  Planarity :  0.004   0.039    622
  Dihedral  :  6.502  49.699    551
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.17 (0.42), residues: 435
  helix: -4.68 (0.49), residues: 28
  sheet: -1.06 (0.46), residues: 135
  loop : -1.27 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG T 498 
 TYR   0.016   0.002   TYR T 453 
 PHE   0.011   0.001   PHE H  90 
 TRP   0.014   0.001   TRP H  36 
 HIS   0.002   0.000   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3518)
  covalent geometry    : angle       0.66953 ( 4795)
  SS BOND              : bond        0.00177 (    6)
  SS BOND              : angle       0.64154 (   12)
  hydrogen bonds       : bond        0.03263 (   91)
  hydrogen bonds       : angle       5.65224 (  222)
  link_BETA1-4         : bond        0.00565 (    1)
  link_BETA1-4         : angle       2.14764 (    3)
  link_NAG-ASN         : bond        0.00814 (    2)
  link_NAG-ASN         : angle       4.97675 (    6)

*********************** 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  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8917 (m100) cc_final: 0.8536 (m100)
REVERT: H   69 ILE cc_start: 0.8921 (mt) cc_final: 0.8684 (mt)
REVERT: H   83 ARG cc_start: 0.7348 (mtm110) cc_final: 0.6843 (mtm110)
REVERT: H   86 ASP cc_start: 0.7729 (m-30) cc_final: 0.6932 (m-30)
REVERT: H  112 ASP cc_start: 0.9098 (t70) cc_final: 0.8850 (t0)
REVERT: L   47 LEU cc_start: 0.8841 (mt) cc_final: 0.8476 (mt)
REVERT: L   61 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7586 (mtp180)
REVERT: L   76 THR cc_start: 0.8558 (t) cc_final: 0.8296 (t)
REVERT: L   95 VAL cc_start: 0.8445 (m) cc_final: 0.8212 (p)
REVERT: T  396 TYR cc_start: 0.8524 (m-80) cc_final: 0.8226 (m-80)
REVERT: T  467 ASP cc_start: 0.7058 (t0) cc_final: 0.6520 (m-30)
REVERT: T  515 PHE cc_start: 0.8688 (m-80) cc_final: 0.8319 (m-10)
REVERT: T  516 GLU cc_start: 0.6772 (tp30) cc_final: 0.6430 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0677
  time to fit residues: 9.3953
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  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3901 r_free = 0.3901 target = 0.165798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.132780 restraints weight = 5873.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.136909 restraints weight = 3717.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.139762 restraints weight = 2677.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.141690 restraints weight = 2115.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.142638 restraints weight = 1788.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   3527  Z= 0.163
  Angle     :  0.723   8.785   4816  Z= 0.356
  Chirality :  0.055   0.302    527
  Planarity :  0.005   0.040    622
  Dihedral  :  6.559  49.231    551
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.10 (0.42), residues: 435
  helix: -4.67 (0.51), residues: 28
  sheet: -1.06 (0.49), residues: 121
  loop : -1.20 (0.40), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  93 
 TYR   0.027   0.002   TYR T 453 
 PHE   0.024   0.002   PHE T 429 
 TRP   0.014   0.002   TRP H  36 
 HIS   0.002   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 3518)
  covalent geometry    : angle       0.70089 ( 4795)
  SS BOND              : bond        0.00174 (    6)
  SS BOND              : angle       0.59789 (   12)
  hydrogen bonds       : bond        0.03375 (   91)
  hydrogen bonds       : angle       5.62359 (  222)
  link_BETA1-4         : bond        0.00479 (    1)
  link_BETA1-4         : angle       2.29776 (    3)
  link_NAG-ASN         : bond        0.00668 (    2)
  link_NAG-ASN         : angle       4.81819 (    6)

*********************** 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
  108 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8897 (m100) cc_final: 0.8474 (m100)
REVERT: H   69 ILE cc_start: 0.8928 (mt) cc_final: 0.8691 (mt)
REVERT: H   83 ARG cc_start: 0.7332 (mtm110) cc_final: 0.6747 (mtm110)
REVERT: H   86 ASP cc_start: 0.7842 (m-30) cc_final: 0.6957 (m-30)
REVERT: H  112 ASP cc_start: 0.9141 (t70) cc_final: 0.8932 (t0)
REVERT: L   47 LEU cc_start: 0.8783 (mt) cc_final: 0.8434 (mt)
REVERT: L   61 ARG cc_start: 0.8281 (mtp180) cc_final: 0.8000 (mtp180)
REVERT: L  104 LEU cc_start: 0.8053 (tp) cc_final: 0.7659 (tt)
REVERT: T  396 TYR cc_start: 0.8599 (m-80) cc_final: 0.8236 (m-80)
REVERT: T  467 ASP cc_start: 0.7063 (t0) cc_final: 0.6404 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0798
  time to fit residues: 10.3005
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  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 13 optimal weight:    0.3980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3888 r_free = 0.3888 target = 0.164769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.131887 restraints weight = 6024.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.136093 restraints weight = 3838.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.138993 restraints weight = 2765.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.140790 restraints weight = 2187.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.141648 restraints weight = 1866.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2565

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= 0.162
  Angle     :  0.724   8.594   4816  Z= 0.356
  Chirality :  0.054   0.311    527
  Planarity :  0.004   0.040    622
  Dihedral  :  6.616  48.952    551
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.42), residues: 435
  helix: -4.50 (0.62), residues: 22
  sheet: -0.96 (0.49), residues: 117
  loop : -1.38 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  38 
 TYR   0.026   0.002   TYR T 453 
 PHE   0.024   0.002   PHE T 429 
 TRP   0.013   0.002   TRP H  47 
 HIS   0.002   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 3518)
  covalent geometry    : angle       0.70279 ( 4795)
  SS BOND              : bond        0.00205 (    6)
  SS BOND              : angle       0.61270 (   12)
  hydrogen bonds       : bond        0.03446 (   91)
  hydrogen bonds       : angle       5.66747 (  222)
  link_BETA1-4         : bond        0.00497 (    1)
  link_BETA1-4         : angle       2.31291 (    3)
  link_NAG-ASN         : bond        0.00632 (    2)
  link_NAG-ASN         : angle       4.78963 (    6)

********************** 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
  105 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8923 (m100) cc_final: 0.8505 (m100)
REVERT: H   83 ARG cc_start: 0.7364 (mtm110) cc_final: 0.7150 (mtm110)
REVERT: H   86 ASP cc_start: 0.7683 (m-30) cc_final: 0.7090 (m-30)
REVERT: H  112 ASP cc_start: 0.9146 (t70) cc_final: 0.8930 (t0)
REVERT: L   47 LEU cc_start: 0.8831 (mt) cc_final: 0.8561 (mt)
REVERT: L   61 ARG cc_start: 0.8276 (mtp180) cc_final: 0.7603 (mtp180)
REVERT: L   76 THR cc_start: 0.8644 (t) cc_final: 0.8391 (t)
REVERT: L  104 LEU cc_start: 0.8002 (tp) cc_final: 0.7664 (tt)
REVERT: T  396 TYR cc_start: 0.8606 (m-80) cc_final: 0.8295 (m-80)
REVERT: T  467 ASP cc_start: 0.7161 (t0) cc_final: 0.6528 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0755
  time to fit residues: 9.6034
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  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 4 optimal weight:    0.2980
   chunk 8 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.164418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131374 restraints weight = 5990.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.135659 restraints weight = 3792.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.138585 restraints weight = 2723.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.140540 restraints weight = 2152.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.141605 restraints weight = 1826.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
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      :  0.004   0.058   3527  Z= 0.156
  Angle     :  0.716   8.684   4816  Z= 0.353
  Chirality :  0.054   0.310    527
  Planarity :  0.004   0.041    622
  Dihedral  :  6.591  49.092    551
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.18 (0.42), residues: 435
  helix: -4.69 (0.50), residues: 28
  sheet: -1.16 (0.49), residues: 121
  loop : -1.24 (0.40), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  93 
 TYR   0.027   0.002   TYR T 473 
 PHE   0.014   0.002   PHE T 371 
 TRP   0.014   0.002   TRP H  36 
 HIS   0.002   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 3518)
  covalent geometry    : angle       0.69510 ( 4795)
  SS BOND              : bond        0.00191 (    6)
  SS BOND              : angle       0.57647 (   12)
  hydrogen bonds       : bond        0.03432 (   91)
  hydrogen bonds       : angle       5.65682 (  222)
  link_BETA1-4         : bond        0.00470 (    1)
  link_BETA1-4         : angle       2.29489 (    3)
  link_NAG-ASN         : bond        0.00622 (    2)
  link_NAG-ASN         : angle       4.75480 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 982.75 seconds
wall clock time: 17 minutes 37.70 seconds (1057.70 seconds total)