Starting phenix.real_space_refine
on Fri Aug 22 17:15:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x95_33067/08_2025/7x95_33067_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x95_33067/08_2025/7x95_33067.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x95_33067/08_2025/7x95_33067_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x95_33067/08_2025/7x95_33067_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x95_33067/08_2025/7x95_33067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x95_33067/08_2025/7x95_33067.map"
  }
  resolution = 3.9
  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=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2137      2.51       5
     N     557      2.21       5
     O     637      1.98       5
     H    3176      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6522
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3043
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 3043
          Classifications: {'peptide': 197}
          Link IDs: {'PTRANS': 11, 'TRANS': 185}
    Chain: "H"
      Number of atoms: 1887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 1887
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
    Chain: "L"
      Number of atoms: 1564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 1564
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
    Chain: "B"
      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
  Time building chain proxies: 1.45, per 1000 atoms: 0.22
  Number of scatterers: 6522
  At special positions: 0
  Unit cell: (90.361, 87.874, 66.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     O     637      8.00
     N     557      7.00
     C    2137      6.00
     H    3176      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  89 " 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 B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 222.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 7 sheets defined
      9.8% alpha, 26.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.591A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.089A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 4.787A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 408
      removed outlier: 4.409A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 405 through 408'
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 4.007A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.203A  pdb=" N   GLU L  84 " --> pdb=" O   SER L  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.500A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS A 378 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 8
    Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.629A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11
    Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AA7, first strand: chain 'L' and resid 46 through 49
      removed outlier: 5.563A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    93 hydrogen bonds defined for protein.
    228 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.18

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3176
        1.03 -     1.23: 10
        1.23 -     1.42: 1526
        1.42 -     1.62: 1883
        1.62 -     1.81: 18
  Bond restraints: 6613
  Sorted by residual:
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.05e+00
  bond pdb=" C5  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.21e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.14e+00
  bond pdb=" C3  NAG B   2 "
       pdb=" O3  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 1.01e+00
  bond pdb=" C3  NAG B   1 "
       pdb=" O3  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.78e-01
  ... (remaining 6608 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 11207
        1.07 -     2.13: 592
        2.13 -     3.20: 33
        3.20 -     4.26: 11
        4.26 -     5.33: 1
  Bond angle restraints: 11844
  Sorted by residual:
  angle pdb=" C   LEU A 518 "
        pdb=" CA  LEU A 518 "
        pdb=" CB  LEU A 518 "
      ideal   model   delta    sigma   weight residual
     116.54  112.37    4.17 1.15e+00 7.56e-01 1.31e+01
  angle pdb=" N   GLY L  15 "
        pdb=" CA  GLY L  15 "
        pdb=" C   GLY L  15 "
      ideal   model   delta    sigma   weight residual
     113.18  118.51   -5.33 2.37e+00 1.78e-01 5.06e+00
  angle pdb=" CA  GLY H   8 "
        pdb=" C   GLY H   8 "
        pdb=" N   GLY H   9 "
      ideal   model   delta    sigma   weight residual
     114.85  116.83   -1.98 9.50e-01 1.11e+00 4.32e+00
  angle pdb=" CA  GLY H   8 "
        pdb=" C   GLY H   8 "
        pdb=" O   GLY H   8 "
      ideal   model   delta    sigma   weight residual
     122.25  120.57    1.68 9.90e-01 1.02e+00 2.87e+00
  angle pdb=" CA  LEU A 518 "
        pdb=" C   LEU A 518 "
        pdb=" N   HIS A 519 "
      ideal   model   delta    sigma   weight residual
     119.52  118.19    1.33 7.90e-01 1.60e+00 2.85e+00
  ... (remaining 11839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 2909
       17.50 -    35.00: 216
       35.00 -    52.50: 80
       52.50 -    70.00: 16
       70.00 -    87.50: 2
  Dihedral angle restraints: 3223
    sinusoidal: 1702
      harmonic: 1521
  Sorted by residual:
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.50  -41.50     1      1.00e+01 1.00e-02 2.41e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   56.62   36.38     1      1.00e+01 1.00e-02 1.87e+01
  dihedral pdb=" CA  LEU L  96 "
           pdb=" C   LEU L  96 "
           pdb=" N   PHE L  97 "
           pdb=" CA  PHE L  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.73  -18.27     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 3220 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 275
       0.026 -    0.053: 153
       0.053 -    0.079: 38
       0.079 -    0.106: 23
       0.106 -    0.132: 16
  Chirality restraints: 505
  Sorted by residual:
  chirality pdb=" CA  ILE A 434 "
            pdb=" N   ILE A 434 "
            pdb=" C   ILE A 434 "
            pdb=" CB  ILE A 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  VAL L  59 "
            pdb=" N   VAL L  59 "
            pdb=" C   VAL L  59 "
            pdb=" CB  VAL L  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  VAL H 122 "
            pdb=" N   VAL H 122 "
            pdb=" C   VAL H 122 "
            pdb=" CB  VAL H 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.19e-01
  ... (remaining 502 not shown)

  Planarity restraints: 1002
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR L  13 "    0.040 5.00e-02 4.00e+02   6.03e-02 5.81e+00
        pdb=" N   PRO L  14 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO L  14 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO L  14 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L   7 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.37e+00
        pdb=" N   PRO L   8 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 462 "    0.017 5.00e-02 4.00e+02   2.58e-02 1.06e+00
        pdb=" N   PRO A 463 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "    0.014 5.00e-02 4.00e+02
  ... (remaining 999 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 508
        2.20 -     2.80: 13089
        2.80 -     3.40: 16606
        3.40 -     4.00: 22671
        4.00 -     4.60: 33900
  Nonbonded interactions: 86774
  Sorted by model distance:
  nonbonded pdb=" H   GLN H 100 "
            pdb=" OD2 ASP H 114 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" O   PHE H  29 "
            pdb="HH22 ARG H  72 "
     model   vdw
     1.623 2.450
  nonbonded pdb="HH22 ARG H  67 "
            pdb=" OD2 ASP H  90 "
     model   vdw
     1.636 2.450
  nonbonded pdb=" OD1 ASP L  86 "
            pdb=" H   THR L 104 "
     model   vdw
     1.647 2.450
  nonbonded pdb=" HZ2 LYS A 417 "
            pdb=" OH  TYR H 109 "
     model   vdw
     1.681 2.450
  ... (remaining 86769 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:             0.220
  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:             0.030
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.640
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3445  Z= 0.125
  Angle     :  0.508   5.329   4694  Z= 0.268
  Chirality :  0.042   0.132    505
  Planarity :  0.004   0.060    598
  Dihedral  : 13.803  87.503   1235
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.00 (0.42), residues: 421
  helix: -1.95 (1.84), residues: 12
  sheet:  0.33 (0.45), residues: 137
  loop : -1.18 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 403 
 TYR   0.012   0.001   TYR A 453 
 PHE   0.008   0.001   PHE A 400 
 TRP   0.012   0.001   TRP L  36 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3437)
  covalent geometry    : angle       0.50263 ( 4676)
  SS BOND              : bond        0.00200 (    6)
  SS BOND              : angle       0.95016 (   12)
  hydrogen bonds       : bond        0.11704 (   93)
  hydrogen bonds       : angle       6.24693 (  228)
  link_BETA1-4         : bond        0.00955 (    1)
  link_BETA1-4         : angle       2.14677 (    3)
  link_NAG-ASN         : bond        0.00009 (    1)
  link_NAG-ASN         : angle       1.39264 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 ASN cc_start: 0.8532 (p0) cc_final: 0.8313 (p0)
REVERT: L   94 ASP cc_start: 0.8508 (t70) cc_final: 0.8297 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1732
  time to fit residues: 16.8269
Evaluate side-chains
  52 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    5.1988

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

Flipped N/Q/H residues before XYZ refinement:
** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  28 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.043284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.035123 restraints weight = 54121.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.037300 restraints weight = 20577.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.038833 restraints weight = 10696.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.039844 restraints weight = 6389.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.040544 restraints weight = 4227.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   3445  Z= 0.210
  Angle     :  0.570   4.945   4694  Z= 0.297
  Chirality :  0.040   0.135    505
  Planarity :  0.004   0.065    598
  Dihedral  :  6.737  52.967    514
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.64 %
    Favored  : 90.25 %
  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: -1.15 (0.41), residues: 421
  helix: -1.81 (1.87), residues: 12
  sheet:  0.17 (0.45), residues: 138
  loop : -1.27 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 355 
 TYR   0.007   0.001   TYR A 489 
 PHE   0.007   0.001   PHE A 515 
 TRP   0.013   0.001   TRP L  98 
 HIS   0.002   0.001   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 3437)
  covalent geometry    : angle       0.56205 ( 4676)
  SS BOND              : bond        0.00238 (    6)
  SS BOND              : angle       1.50505 (   12)
  hydrogen bonds       : bond        0.03537 (   93)
  hydrogen bonds       : angle       5.83810 (  228)
  link_BETA1-4         : bond        0.00018 (    1)
  link_BETA1-4         : angle       1.33672 (    3)
  link_NAG-ASN         : bond        0.00380 (    1)
  link_NAG-ASN         : angle       2.12207 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.9446 (pt) cc_final: 0.9083 (pt)
REVERT: A  406 GLU cc_start: 0.8866 (pt0) cc_final: 0.8325 (pp20)
REVERT: A  417 LYS cc_start: 0.9385 (mmmm) cc_final: 0.8867 (ttmm)
REVERT: A  465 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6926 (tm-30)
REVERT: H   34 MET cc_start: 0.9174 (mmm) cc_final: 0.8721 (mmm)
  outliers start: 4
  outliers final: 3
  residues processed: 59
  average time/residue: 0.1359
  time to fit residues: 9.7582
Evaluate side-chains
  52 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain L residue   28 ASN
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
H 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.043532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.035478 restraints weight = 53984.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.037656 restraints weight = 20547.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.039154 restraints weight = 10597.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.040180 restraints weight = 6355.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.040866 restraints weight = 4185.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3445  Z= 0.160
  Angle     :  0.552   4.932   4694  Z= 0.286
  Chirality :  0.041   0.142    505
  Planarity :  0.004   0.064    598
  Dihedral  :  6.167  44.844    514
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 10.86 %
    Favored  : 88.30 %
  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: -1.07 (0.41), residues: 421
  helix: -1.56 (1.98), residues: 12
  sheet:  0.15 (0.45), residues: 136
  loop : -1.17 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 403 
 TYR   0.006   0.001   TYR L  88 
 PHE   0.007   0.001   PHE A 456 
 TRP   0.007   0.001   TRP L  98 
 HIS   0.002   0.001   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3437)
  covalent geometry    : angle       0.54697 ( 4676)
  SS BOND              : bond        0.00276 (    6)
  SS BOND              : angle       1.26269 (   12)
  hydrogen bonds       : bond        0.03305 (   93)
  hydrogen bonds       : angle       5.71438 (  228)
  link_BETA1-4         : bond        0.00329 (    1)
  link_BETA1-4         : angle       1.27600 (    3)
  link_NAG-ASN         : bond        0.00168 (    1)
  link_NAG-ASN         : angle       1.69724 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.9421 (pt) cc_final: 0.9087 (pt)
REVERT: A  406 GLU cc_start: 0.8841 (pt0) cc_final: 0.8300 (pp20)
REVERT: A  417 LYS cc_start: 0.9400 (mmmm) cc_final: 0.8947 (ttmm)
REVERT: A  465 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6945 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 58
  average time/residue: 0.1282
  time to fit residues: 9.0021
Evaluate side-chains
  54 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 29 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 3 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** H 106 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 = 0.2880 r_free = 0.2880 target = 0.041716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.033839 restraints weight = 56256.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.035915 restraints weight = 21344.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.037388 restraints weight = 11068.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.038367 restraints weight = 6592.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.039038 restraints weight = 4364.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   3445  Z= 0.235
  Angle     :  0.582   6.088   4694  Z= 0.302
  Chirality :  0.040   0.136    505
  Planarity :  0.004   0.064    598
  Dihedral  :  5.858  45.052    514
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.70 %
    Favored  : 87.19 %
  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: -1.09 (0.41), residues: 421
  helix: -1.81 (1.82), residues: 12
  sheet:  0.29 (0.47), residues: 133
  loop : -1.26 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 403 
 TYR   0.008   0.001   TYR A 365 
 PHE   0.009   0.001   PHE A 456 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.003   0.001   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 3437)
  covalent geometry    : angle       0.57158 ( 4676)
  SS BOND              : bond        0.00974 (    6)
  SS BOND              : angle       1.96137 (   12)
  hydrogen bonds       : bond        0.03528 (   93)
  hydrogen bonds       : angle       5.85636 (  228)
  link_BETA1-4         : bond        0.00271 (    1)
  link_BETA1-4         : angle       1.01891 (    3)
  link_NAG-ASN         : bond        0.00486 (    1)
  link_NAG-ASN         : angle       1.91228 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9434 (mmmm) cc_final: 0.9056 (ttmm)
REVERT: A  465 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7086 (tm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 51
  average time/residue: 0.1470
  time to fit residues: 9.1292
Evaluate side-chains
  51 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    2.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
H 106 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.042341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.034269 restraints weight = 55686.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.036405 restraints weight = 21270.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.037912 restraints weight = 11044.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.038921 restraints weight = 6649.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.039622 restraints weight = 4408.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3445  Z= 0.132
  Angle     :  0.542   5.147   4694  Z= 0.280
  Chirality :  0.041   0.144    505
  Planarity :  0.004   0.062    598
  Dihedral  :  5.409  43.088    514
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 12.81 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.02 (0.41), residues: 421
  helix: -1.49 (1.97), residues: 12
  sheet:  0.30 (0.46), residues: 133
  loop : -1.19 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 403 
 TYR   0.005   0.001   TYR H 111 
 PHE   0.010   0.001   PHE A 456 
 TRP   0.005   0.001   TRP L  98 
 HIS   0.001   0.000   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3437)
  covalent geometry    : angle       0.53601 ( 4676)
  SS BOND              : bond        0.00519 (    6)
  SS BOND              : angle       1.53857 (   12)
  hydrogen bonds       : bond        0.03200 (   93)
  hydrogen bonds       : angle       5.65320 (  228)
  link_BETA1-4         : bond        0.00150 (    1)
  link_BETA1-4         : angle       0.94412 (    3)
  link_NAG-ASN         : bond        0.00105 (    1)
  link_NAG-ASN         : angle       1.34687 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9427 (mmmm) cc_final: 0.9027 (ttmm)
REVERT: A  465 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7015 (tm-30)
REVERT: L   86 ASP cc_start: 0.7771 (p0) cc_final: 0.7444 (p0)
  outliers start: 4
  outliers final: 1
  residues processed: 55
  average time/residue: 0.1372
  time to fit residues: 9.1641
Evaluate side-chains
  52 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** H 106 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 = 0.2880 r_free = 0.2880 target = 0.041533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.033616 restraints weight = 55764.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.035645 restraints weight = 21171.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.037091 restraints weight = 11155.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.038055 restraints weight = 6716.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.038749 restraints weight = 4504.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.3325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3445  Z= 0.203
  Angle     :  0.571   5.262   4694  Z= 0.296
  Chirality :  0.041   0.153    505
  Planarity :  0.004   0.061    598
  Dihedral  :  5.421  44.091    514
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 13.37 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.10 (0.40), residues: 421
  helix: -1.64 (1.45), residues: 18
  sheet:  0.28 (0.46), residues: 133
  loop : -1.24 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 403 
 TYR   0.007   0.001   TYR A 365 
 PHE   0.008   0.001   PHE A 456 
 TRP   0.017   0.002   TRP H  36 
 HIS   0.002   0.001   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 3437)
  covalent geometry    : angle       0.56430 ( 4676)
  SS BOND              : bond        0.00556 (    6)
  SS BOND              : angle       1.57511 (   12)
  hydrogen bonds       : bond        0.03496 (   93)
  hydrogen bonds       : angle       5.78405 (  228)
  link_BETA1-4         : bond        0.00226 (    1)
  link_BETA1-4         : angle       0.84540 (    3)
  link_NAG-ASN         : bond        0.00375 (    1)
  link_NAG-ASN         : angle       1.63192 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9464 (mmmm) cc_final: 0.9089 (ttmm)
REVERT: A  465 GLU cc_start: 0.7434 (tm-30) cc_final: 0.6665 (tm-30)
  outliers start: 3
  outliers final: 3
  residues processed: 51
  average time/residue: 0.1717
  time to fit residues: 10.4278
Evaluate side-chains
  52 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain L residue   28 ASN
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.042236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.034099 restraints weight = 54520.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.036197 restraints weight = 20947.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.037673 restraints weight = 10943.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.038702 restraints weight = 6650.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.039384 restraints weight = 4414.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3445  Z= 0.125
  Angle     :  0.558   6.096   4694  Z= 0.283
  Chirality :  0.042   0.152    505
  Planarity :  0.004   0.061    598
  Dihedral  :  5.129  41.986    514
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 14.21 %
    Favored  : 84.96 %
  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: -1.02 (0.41), residues: 421
  helix: -1.75 (1.44), residues: 18
  sheet:  0.31 (0.46), residues: 133
  loop : -1.16 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 403 
 TYR   0.006   0.001   TYR H 111 
 PHE   0.009   0.001   PHE A 456 
 TRP   0.015   0.001   TRP H  36 
 HIS   0.002   0.001   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3437)
  covalent geometry    : angle       0.55338 ( 4676)
  SS BOND              : bond        0.00359 (    6)
  SS BOND              : angle       1.37791 (   12)
  hydrogen bonds       : bond        0.03201 (   93)
  hydrogen bonds       : angle       5.69075 (  228)
  link_BETA1-4         : bond        0.00251 (    1)
  link_BETA1-4         : angle       0.96208 (    3)
  link_NAG-ASN         : bond        0.00010 (    1)
  link_NAG-ASN         : angle       1.24363 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9459 (mmmm) cc_final: 0.9083 (ttmm)
REVERT: A  465 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7017 (tm-30)
REVERT: H  113 MET cc_start: 0.8710 (ttm) cc_final: 0.8425 (tpt)
REVERT: L   86 ASP cc_start: 0.7757 (p0) cc_final: 0.7427 (p0)
  outliers start: 3
  outliers final: 1
  residues processed: 57
  average time/residue: 0.1435
  time to fit residues: 9.9359
Evaluate side-chains
  54 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 33 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:    0.2980
   overall best weight:    3.4386

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

Flipped N/Q/H residues before XYZ refinement:
** H 106 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 = 0.2890 r_free = 0.2890 target = 0.041734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.033726 restraints weight = 56207.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.035794 restraints weight = 21578.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.037263 restraints weight = 11251.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.038221 restraints weight = 6826.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.038935 restraints weight = 4595.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3445  Z= 0.152
  Angle     :  0.572   6.755   4694  Z= 0.293
  Chirality :  0.041   0.148    505
  Planarity :  0.004   0.060    598
  Dihedral  :  5.078  42.405    514
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 15.04 %
    Favored  : 84.68 %
  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: -1.13 (0.40), residues: 421
  helix: -1.94 (1.41), residues: 18
  sheet:  0.19 (0.45), residues: 135
  loop : -1.21 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 403 
 TYR   0.006   0.001   TYR H 111 
 PHE   0.007   0.001   PHE A 456 
 TRP   0.013   0.001   TRP H  36 
 HIS   0.002   0.001   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3437)
  covalent geometry    : angle       0.55982 ( 4676)
  SS BOND              : bond        0.00427 (    6)
  SS BOND              : angle       2.27178 (   12)
  hydrogen bonds       : bond        0.03222 (   93)
  hydrogen bonds       : angle       5.68586 (  228)
  link_BETA1-4         : bond        0.00237 (    1)
  link_BETA1-4         : angle       0.99578 (    3)
  link_NAG-ASN         : bond        0.00209 (    1)
  link_NAG-ASN         : angle       1.51352 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.8914 (pt0) cc_final: 0.8385 (pp20)
REVERT: A  417 LYS cc_start: 0.9472 (mmmm) cc_final: 0.9081 (ttmm)
REVERT: A  465 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7058 (tm-30)
REVERT: H  113 MET cc_start: 0.8707 (ttm) cc_final: 0.8409 (tpt)
REVERT: L   86 ASP cc_start: 0.7798 (p0) cc_final: 0.7480 (p0)
  outliers start: 1
  outliers final: 1
  residues processed: 53
  average time/residue: 0.1634
  time to fit residues: 10.4432
Evaluate side-chains
  54 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
H 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.042364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.034212 restraints weight = 55717.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.036328 restraints weight = 21382.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.037814 restraints weight = 11194.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.038818 restraints weight = 6771.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.039565 restraints weight = 4541.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3445  Z= 0.107
  Angle     :  0.568   7.495   4694  Z= 0.287
  Chirality :  0.042   0.148    505
  Planarity :  0.004   0.061    598
  Dihedral  :  4.802  39.759    514
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 15.60 %
    Favored  : 83.84 %
  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: -1.02 (0.41), residues: 421
  helix: -2.11 (1.41), residues: 18
  sheet:  0.26 (0.45), residues: 135
  loop : -1.11 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.006   0.001   TYR H 111 
 PHE   0.009   0.001   PHE A 456 
 TRP   0.012   0.001   TRP H  36 
 HIS   0.001   0.000   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 3437)
  covalent geometry    : angle       0.55820 ( 4676)
  SS BOND              : bond        0.00256 (    6)
  SS BOND              : angle       1.99805 (   12)
  hydrogen bonds       : bond        0.03035 (   93)
  hydrogen bonds       : angle       5.61479 (  228)
  link_BETA1-4         : bond        0.00443 (    1)
  link_BETA1-4         : angle       1.06757 (    3)
  link_NAG-ASN         : bond        0.00075 (    1)
  link_NAG-ASN         : angle       1.16600 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.8936 (pt0) cc_final: 0.8468 (pp20)
REVERT: A  417 LYS cc_start: 0.9468 (mmmm) cc_final: 0.9097 (ttmm)
REVERT: A  465 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7114 (tm-30)
REVERT: H  113 MET cc_start: 0.8657 (ttm) cc_final: 0.8360 (tpt)
REVERT: L   86 ASP cc_start: 0.7739 (p0) cc_final: 0.7421 (p0)
  outliers start: 2
  outliers final: 2
  residues processed: 55
  average time/residue: 0.1323
  time to fit residues: 8.8587
Evaluate side-chains
  55 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  106 GLN
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0470
   chunk 13 optimal weight:    7.9990
   chunk 38 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 29 optimal weight:    7.9990
   overall best weight:    4.2086

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

Flipped N/Q/H residues before XYZ refinement:
H 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.042302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.034184 restraints weight = 54175.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.036295 restraints weight = 20888.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.037779 restraints weight = 10975.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.038784 restraints weight = 6644.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.039424 restraints weight = 4433.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.134   3445  Z= 0.179
  Angle     :  1.232  59.198   4694  Z= 0.725
  Chirality :  0.042   0.146    505
  Planarity :  0.004   0.060    598
  Dihedral  :  4.796  39.803    514
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 15.88 %
    Favored  : 83.57 %
  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: -1.02 (0.41), residues: 421
  helix: -2.11 (1.42), residues: 18
  sheet:  0.26 (0.45), residues: 135
  loop : -1.11 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.006   0.001   TYR A 453 
 PHE   0.009   0.001   PHE A 456 
 TRP   0.012   0.001   TRP H  36 
 HIS   0.001   0.001   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 3437)
  covalent geometry    : angle       1.22591 ( 4676)
  SS BOND              : bond        0.00252 (    6)
  SS BOND              : angle       2.64140 (   12)
  hydrogen bonds       : bond        0.03097 (   93)
  hydrogen bonds       : angle       5.61706 (  228)
  link_BETA1-4         : bond        0.00592 (    1)
  link_BETA1-4         : angle       1.17284 (    3)
  link_NAG-ASN         : bond        0.00029 (    1)
  link_NAG-ASN         : angle       1.19177 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.8938 (pt0) cc_final: 0.8467 (pp20)
REVERT: A  417 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9106 (ttmm)
REVERT: A  465 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7086 (tm-30)
REVERT: H  113 MET cc_start: 0.8666 (ttm) cc_final: 0.8362 (tpt)
REVERT: L   86 ASP cc_start: 0.7729 (p0) cc_final: 0.7413 (p0)
  outliers start: 2
  outliers final: 1
  residues processed: 54
  average time/residue: 0.1617
  time to fit residues: 10.4491
Evaluate side-chains
  55 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:   20.0000
   chunk 22 optimal weight:    7.9990
   chunk 31 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** H 106 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 = 0.2905 r_free = 0.2905 target = 0.042191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.034067 restraints weight = 54750.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.036182 restraints weight = 21073.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.037652 restraints weight = 11011.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.038642 restraints weight = 6666.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.039387 restraints weight = 4480.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.134   3445  Z= 0.179
  Angle     :  1.232  59.198   4694  Z= 0.725
  Chirality :  0.042   0.146    505
  Planarity :  0.004   0.060    598
  Dihedral  :  4.796  39.803    514
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 15.88 %
    Favored  : 83.84 %
  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: -1.02 (0.41), residues: 421
  helix: -2.11 (1.42), residues: 18
  sheet:  0.26 (0.45), residues: 135
  loop : -1.11 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.006   0.001   TYR A 453 
 PHE   0.009   0.001   PHE A 456 
 TRP   0.012   0.001   TRP H  36 
 HIS   0.001   0.001   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 3437)
  covalent geometry    : angle       1.22591 ( 4676)
  SS BOND              : bond        0.00252 (    6)
  SS BOND              : angle       2.64140 (   12)
  hydrogen bonds       : bond        0.03097 (   93)
  hydrogen bonds       : angle       5.61706 (  228)
  link_BETA1-4         : bond        0.00592 (    1)
  link_BETA1-4         : angle       1.17284 (    3)
  link_NAG-ASN         : bond        0.00029 (    1)
  link_NAG-ASN         : angle       1.19177 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1367.71 seconds
wall clock time: 23 minutes 54.94 seconds (1434.94 seconds total)