Starting phenix.real_space_refine
on Fri May  9 18:31:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d8r_27255/05_2025/8d8r_27255.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d8r_27255/05_2025/8d8r_27255.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d8r_27255/05_2025/8d8r_27255.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d8r_27255/05_2025/8d8r_27255.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d8r_27255/05_2025/8d8r_27255.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d8r_27255/05_2025/8d8r_27255.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.039
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      19      5.16       5
     C    2102      2.51       5
     N     562      2.21       5
     O     640      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3323
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 832
          Classifications: {'peptide': 109}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 941
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.14, per 1000 atoms: 0.94
  Number of scatterers: 3323
  At special positions: 0
  Unit cell: (69.564, 59.024, 102.238, 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      19     16.00
     O     640      8.00
     N     562      7.00
     C    2102      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 H  97 " - pdb=" SG  CYS H 102 " distance=2.19
    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=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.08
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.21

  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
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 395.7 milliseconds
  

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  776

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 9 sheets defined
      15.1% alpha, 31.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.590A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 60 through 64
    Processing helix  chain 'H' and resid 73 through 75
      No H-bonds generated for 'chain 'H' and resid 73 through 75'
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 3.799A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.510A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.449A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.531A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
    Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.510A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.612A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474

    119 hydrogen bonds defined for protein.
    267 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: 0.85

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 863
        1.33 -     1.46: 844
        1.46 -     1.58: 1674
        1.58 -     1.71: 0
        1.71 -     1.83: 24
  Bond restraints: 3405
  Sorted by residual:
  bond pdb=" CB  PHE H 106 "
       pdb=" CG  PHE H 106 "
    ideal  model  delta    sigma   weight residual
    1.502  1.444  0.058 2.30e-02 1.89e+03 6.34e+00
  bond pdb=" CG  ASP L  82 "
       pdb=" OD2 ASP L  82 "
    ideal  model  delta    sigma   weight residual
    1.249  1.204  0.045 1.90e-02 2.77e+03 5.51e+00
  bond pdb=" CD  GLU H  10 "
       pdb=" OE1 GLU H  10 "
    ideal  model  delta    sigma   weight residual
    1.249  1.205  0.044 1.90e-02 2.77e+03 5.46e+00
  bond pdb=" CB  VAL A 350 "
       pdb=" CG1 VAL A 350 "
    ideal  model  delta    sigma   weight residual
    1.521  1.445  0.076 3.30e-02 9.18e+02 5.29e+00
  bond pdb=" CG  ASP A 389 "
       pdb=" OD2 ASP A 389 "
    ideal  model  delta    sigma   weight residual
    1.249  1.205  0.044 1.90e-02 2.77e+03 5.29e+00
  ... (remaining 3400 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 3935
        1.62 -     3.24: 561
        3.24 -     4.85: 95
        4.85 -     6.47: 24
        6.47 -     8.09: 7
  Bond angle restraints: 4622
  Sorted by residual:
  angle pdb=" C   ALA H  94 "
        pdb=" N   PRO H  95 "
        pdb=" CA  PRO H  95 "
      ideal   model   delta    sigma   weight residual
     119.78  127.87   -8.09 1.03e+00 9.43e-01 6.17e+01
  angle pdb=" C   GLY H   8 "
        pdb=" N   PRO H   9 "
        pdb=" CA  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     119.76  127.18   -7.42 1.03e+00 9.43e-01 5.19e+01
  angle pdb=" C   ILE L  58 "
        pdb=" N   PRO L  59 "
        pdb=" CA  PRO L  59 "
      ideal   model   delta    sigma   weight residual
     119.78  126.71   -6.93 1.03e+00 9.43e-01 4.53e+01
  angle pdb=" C   SER A 383 "
        pdb=" N   PRO A 384 "
        pdb=" CA  PRO A 384 "
      ideal   model   delta    sigma   weight residual
     119.56  126.31   -6.75 1.02e+00 9.61e-01 4.38e+01
  angle pdb=" C   GLN A 498 "
        pdb=" N   PRO A 499 "
        pdb=" CA  PRO A 499 "
      ideal   model   delta    sigma   weight residual
     119.56  125.98   -6.42 1.02e+00 9.61e-01 3.96e+01
  ... (remaining 4617 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.51: 1933
       16.51 -    33.03: 61
       33.03 -    49.54: 15
       49.54 -    66.05: 7
       66.05 -    82.56: 6
  Dihedral angle restraints: 2022
    sinusoidal: 798
      harmonic: 1224
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.99  -52.99     1      1.00e+01 1.00e-02 3.82e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  92 "
           pdb=" CB  CYS H  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.61   37.39     1      1.00e+01 1.00e-02 1.97e+01
  dihedral pdb=" CA  ALA H  94 "
           pdb=" C   ALA H  94 "
           pdb=" N   PRO H  95 "
           pdb=" CA  PRO H  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.74   21.26     0      5.00e+00 4.00e-02 1.81e+01
  ... (remaining 2019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 274
       0.041 -    0.081: 153
       0.081 -    0.122: 51
       0.122 -    0.163: 16
       0.163 -    0.203: 4
  Chirality restraints: 498
  Sorted by residual:
  chirality pdb=" CA  VAL H  37 "
            pdb=" N   VAL H  37 "
            pdb=" C   VAL H  37 "
            pdb=" CB  VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  ASN H 103 "
            pdb=" N   ASN H 103 "
            pdb=" C   ASN H 103 "
            pdb=" CB  ASN H 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.45e-01
  chirality pdb=" CB  ILE A 402 "
            pdb=" CA  ILE A 402 "
            pdb=" CG1 ILE A 402 "
            pdb=" CG2 ILE A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.24e-01
  ... (remaining 495 not shown)

  Planarity restraints: 597
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 423 "    0.045 2.00e-02 2.50e+03   2.45e-02 1.20e+01
        pdb=" CG  TYR A 423 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 423 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 423 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 423 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 423 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 423 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 423 "    0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU L  78 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.77e+00
        pdb=" C   LEU L  78 "    0.034 2.00e-02 2.50e+03
        pdb=" O   LEU L  78 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU L  79 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 488 "    0.009 2.00e-02 2.50e+03   1.88e-02 3.54e+00
        pdb=" C   CYS A 488 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   CYS A 488 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TYR A 489 "    0.011 2.00e-02 2.50e+03
  ... (remaining 594 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 1757
        2.99 -     3.47: 2933
        3.47 -     3.94: 5421
        3.94 -     4.42: 6051
        4.42 -     4.90: 9996
  Nonbonded interactions: 26158
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.512 3.040
  nonbonded pdb=" O   LYS H  13 "
            pdb=" OG1 THR H  16 "
     model   vdw
     2.538 3.040
  nonbonded pdb=" N   TYR A 380 "
            pdb=" N   GLY A 381 "
     model   vdw
     2.550 2.560
  nonbonded pdb=" O   SER H  31 "
            pdb=" OG  SER H 101 "
     model   vdw
     2.554 3.040
  nonbonded pdb=" OG  SER H  98 "
            pdb=" N   SER H  99 "
     model   vdw
     2.556 3.120
  ... (remaining 26153 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.890
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.080
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6153
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      :  0.012   0.183   3412  Z= 0.636
  Angle     :  1.263   8.091   4637  Z= 0.872
  Chirality :  0.056   0.203    498
  Planarity :  0.006   0.024    596
  Dihedral  : 10.916  82.563   1228
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 1.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.43), residues: 419
  helix: -4.23 (0.36), residues: 34
  sheet:  1.42 (0.42), residues: 150
  loop :  2.42 (0.44), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.005   TRP H  47 
 HIS   0.002   0.001   HIS L  90 
 PHE   0.016   0.004   PHE A 400 
 TYR   0.045   0.005   TYR A 423 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.07200 (    1)
  link_NAG-ASN         : angle       1.35761 (    3)
  hydrogen bonds       : bond        0.18158 (  112)
  hydrogen bonds       : angle       9.30121 (  267)
  SS BOND              : bond        0.10135 (    6)
  SS BOND              : angle       3.11307 (   12)
  covalent geometry    : bond        0.01100 ( 3405)
  covalent geometry    : angle       1.25470 ( 4622)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    2 ILE cc_start: 0.7054 (mm) cc_final: 0.6774 (mm)
REVERT: H   20 VAL cc_start: 0.8368 (t) cc_final: 0.7917 (p)
REVERT: H   57 THR cc_start: 0.6787 (p) cc_final: 0.6535 (t)
REVERT: A  354 ASN cc_start: 0.7161 (t0) cc_final: 0.6751 (p0)
REVERT: A  427 ASP cc_start: 0.8005 (m-30) cc_final: 0.7564 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1810
  time to fit residues: 26.7669
Evaluate side-chains
  76 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 10 optimal weight:    0.1980
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
H  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.193651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.170814 restraints weight = 6309.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.175579 restraints weight = 4041.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.178851 restraints weight = 2840.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6312
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3412  Z= 0.182
  Angle     :  0.657   5.962   4637  Z= 0.363
  Chirality :  0.044   0.130    498
  Planarity :  0.005   0.059    596
  Dihedral  :  5.121  18.594    491
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  1.39 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.42), residues: 419
  helix: -3.63 (0.64), residues: 28
  sheet:  0.86 (0.40), residues: 158
  loop :  1.47 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP H  36 
 HIS   0.001   0.001   HIS L  90 
 PHE   0.039   0.003   PHE A 400 
 TYR   0.017   0.002   TYR A 453 
 ARG   0.004   0.001   ARG H  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00389 (    1)
  link_NAG-ASN         : angle       1.47797 (    3)
  hydrogen bonds       : bond        0.04606 (  112)
  hydrogen bonds       : angle       6.97473 (  267)
  SS BOND              : bond        0.00427 (    6)
  SS BOND              : angle       0.45872 (   12)
  covalent geometry    : bond        0.00405 ( 3405)
  covalent geometry    : angle       0.65628 ( 4622)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   20 VAL cc_start: 0.8713 (t) cc_final: 0.8482 (t)
REVERT: H   36 TRP cc_start: 0.8538 (m100) cc_final: 0.8018 (m100)
REVERT: H   80 MET cc_start: 0.4226 (ptm) cc_final: 0.3752 (ptm)
REVERT: A  370 ASN cc_start: 0.7067 (m-40) cc_final: 0.6802 (p0)
REVERT: A  403 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7423 (mtm110)
REVERT: A  427 ASP cc_start: 0.8029 (m-30) cc_final: 0.7529 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1439
  time to fit residues: 17.8305
Evaluate side-chains
  84 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 39 optimal weight:    0.4980
   chunk 33 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.184359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.161304 restraints weight = 6151.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.165639 restraints weight = 3971.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.168779 restraints weight = 2844.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6666
moved from start:          0.5977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   3412  Z= 0.235
  Angle     :  0.712   7.850   4637  Z= 0.394
  Chirality :  0.048   0.265    498
  Planarity :  0.006   0.052    596
  Dihedral  :  5.982  32.808    491
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  4.43 %
    Favored  : 95.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.42), residues: 419
  helix: -3.65 (0.63), residues: 28
  sheet:  0.31 (0.40), residues: 155
  loop :  0.69 (0.43), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP L  96 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.024   0.003   PHE A 400 
 TYR   0.028   0.003   TYR L  32 
 ARG   0.008   0.001   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00635 (    1)
  link_NAG-ASN         : angle       2.09386 (    3)
  hydrogen bonds       : bond        0.04440 (  112)
  hydrogen bonds       : angle       7.28215 (  267)
  SS BOND              : bond        0.01656 (    6)
  SS BOND              : angle       1.89562 (   12)
  covalent geometry    : bond        0.00532 ( 3405)
  covalent geometry    : angle       0.70451 ( 4622)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8796 (m100) cc_final: 0.8527 (m100)
REVERT: H   80 MET cc_start: 0.4926 (ptm) cc_final: 0.4307 (ptm)
REVERT: H  111 GLN cc_start: 0.7698 (pm20) cc_final: 0.7452 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1469
  time to fit residues: 17.4606
Evaluate side-chains
  77 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0870
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
L  90 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.186713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.164422 restraints weight = 6430.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.168848 restraints weight = 4177.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.171905 restraints weight = 2980.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6664
moved from start:          0.6683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   3412  Z= 0.177
  Angle     :  0.633   7.994   4637  Z= 0.343
  Chirality :  0.047   0.264    498
  Planarity :  0.005   0.049    596
  Dihedral  :  5.609  35.834    491
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  1.66 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.42), residues: 419
  helix: -3.45 (0.71), residues: 28
  sheet:  0.50 (0.40), residues: 152
  loop :  0.45 (0.43), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP L  96 
 HIS   0.002   0.001   HIS L  90 
 PHE   0.017   0.002   PHE H  29 
 TYR   0.020   0.002   TYR L  32 
 ARG   0.005   0.001   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00586 (    1)
  link_NAG-ASN         : angle       3.73364 (    3)
  hydrogen bonds       : bond        0.03802 (  112)
  hydrogen bonds       : angle       6.73908 (  267)
  SS BOND              : bond        0.01023 (    6)
  SS BOND              : angle       2.10871 (   12)
  covalent geometry    : bond        0.00414 ( 3405)
  covalent geometry    : angle       0.61753 ( 4622)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   91 TYR cc_start: 0.7428 (m-10) cc_final: 0.6615 (m-10)
REVERT: H   68 THR cc_start: 0.6740 (m) cc_final: 0.6483 (t)
REVERT: H   80 MET cc_start: 0.4916 (ptm) cc_final: 0.4185 (ptm)
REVERT: H  111 GLN cc_start: 0.7684 (pm20) cc_final: 0.7301 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1687
  time to fit residues: 18.9085
Evaluate side-chains
  81 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    0.4980
   chunk 23 optimal weight:    0.1980
   chunk 29 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 4 optimal weight:    0.3980
   chunk 18 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.187434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.164926 restraints weight = 6354.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.169234 restraints weight = 4159.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.172217 restraints weight = 3001.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6659
moved from start:          0.7077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3412  Z= 0.163
  Angle     :  0.614  10.515   4637  Z= 0.337
  Chirality :  0.046   0.266    498
  Planarity :  0.005   0.047    596
  Dihedral  :  5.507  35.362    491
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.42), residues: 419
  helix: -3.16 (0.80), residues: 27
  sheet:  0.54 (0.42), residues: 146
  loop :  0.15 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP H  36 
 HIS   0.009   0.003   HIS L  90 
 PHE   0.029   0.002   PHE H  29 
 TYR   0.017   0.002   TYR A 453 
 ARG   0.004   0.001   ARG A 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00599 (    1)
  link_NAG-ASN         : angle       2.33393 (    3)
  hydrogen bonds       : bond        0.03806 (  112)
  hydrogen bonds       : angle       6.72422 (  267)
  SS BOND              : bond        0.00976 (    6)
  SS BOND              : angle       1.54629 (   12)
  covalent geometry    : bond        0.00366 ( 3405)
  covalent geometry    : angle       0.60709 ( 4622)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8587 (m100) cc_final: 0.8198 (m100)
REVERT: H   45 LEU cc_start: 0.8463 (mt) cc_final: 0.8248 (mt)
REVERT: H   80 MET cc_start: 0.5157 (ptm) cc_final: 0.4539 (ptm)
REVERT: H  111 GLN cc_start: 0.7764 (pm20) cc_final: 0.7456 (pt0)
REVERT: A  473 TYR cc_start: 0.8285 (t80) cc_final: 0.8015 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1470
  time to fit residues: 15.7044
Evaluate side-chains
  77 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0870
   chunk 17 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7560

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.183647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.160482 restraints weight = 6364.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.164785 restraints weight = 4103.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.167830 restraints weight = 2927.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6778
moved from start:          0.7733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   3412  Z= 0.205
  Angle     :  0.655   9.697   4637  Z= 0.358
  Chirality :  0.048   0.240    498
  Planarity :  0.005   0.044    596
  Dihedral  :  5.867  30.063    491
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.42), residues: 419
  helix: -3.47 (0.66), residues: 29
  sheet:  0.30 (0.42), residues: 146
  loop : -0.03 (0.43), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP L  96 
 HIS   0.004   0.002   HIS L  90 
 PHE   0.033   0.002   PHE A 400 
 TYR   0.017   0.002   TYR A 453 
 ARG   0.003   0.001   ARG A 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00787 (    1)
  link_NAG-ASN         : angle       2.04035 (    3)
  hydrogen bonds       : bond        0.04006 (  112)
  hydrogen bonds       : angle       7.05945 (  267)
  SS BOND              : bond        0.00416 (    6)
  SS BOND              : angle       1.38020 (   12)
  covalent geometry    : bond        0.00467 ( 3405)
  covalent geometry    : angle       0.65048 ( 4622)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: H   30 MET cc_start: 0.8815 (mmm) cc_final: 0.8585 (mmm)
REVERT: H   36 TRP cc_start: 0.8733 (m100) cc_final: 0.8382 (m100)
REVERT: H   80 MET cc_start: 0.5254 (ptm) cc_final: 0.4788 (ptm)
REVERT: H  111 GLN cc_start: 0.7843 (pm20) cc_final: 0.7535 (pt0)
REVERT: A  402 ILE cc_start: 0.8744 (pt) cc_final: 0.8522 (pt)
REVERT: A  403 ARG cc_start: 0.8353 (mtp85) cc_final: 0.8043 (mtp-110)
REVERT: A  473 TYR cc_start: 0.8385 (t80) cc_final: 0.8070 (t80)
REVERT: A  516 GLU cc_start: 0.6304 (tt0) cc_final: 0.6048 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1624
  time to fit residues: 16.9741
Evaluate side-chains
  74 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 29 optimal weight:    0.3980
   chunk 14 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.183720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.161436 restraints weight = 6577.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.165472 restraints weight = 4360.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.168394 restraints weight = 3187.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6794
moved from start:          0.8020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3412  Z= 0.196
  Angle     :  0.656   9.941   4637  Z= 0.357
  Chirality :  0.048   0.224    498
  Planarity :  0.005   0.044    596
  Dihedral  :  5.969  33.257    491
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.42), residues: 419
  helix: -3.26 (0.73), residues: 29
  sheet:  0.25 (0.44), residues: 138
  loop : -0.21 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP H  50 
 HIS   0.003   0.001   HIS L  90 
 PHE   0.016   0.002   PHE A 400 
 TYR   0.029   0.002   TYR A 453 
 ARG   0.005   0.001   ARG L  45 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00607 (    1)
  link_NAG-ASN         : angle       2.12251 (    3)
  hydrogen bonds       : bond        0.03883 (  112)
  hydrogen bonds       : angle       7.13093 (  267)
  SS BOND              : bond        0.00821 (    6)
  SS BOND              : angle       1.37381 (   12)
  covalent geometry    : bond        0.00439 ( 3405)
  covalent geometry    : angle       0.65097 ( 4622)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8737 (m100) cc_final: 0.8319 (m100)
REVERT: H   80 MET cc_start: 0.5154 (ptm) cc_final: 0.4715 (ptm)
REVERT: H  111 GLN cc_start: 0.7945 (pm20) cc_final: 0.7584 (pt0)
REVERT: A  403 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7918 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1739
  time to fit residues: 19.6663
Evaluate side-chains
  79 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 24 optimal weight:    0.1980
   chunk 17 optimal weight:    0.7980
   chunk 21 optimal weight:    0.2980
   chunk 14 optimal weight:    0.0030
   chunk 20 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.3390

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.188354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.166601 restraints weight = 6440.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.170734 restraints weight = 4174.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.173620 restraints weight = 2989.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.8150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3412  Z= 0.127
  Angle     :  0.591   8.447   4637  Z= 0.316
  Chirality :  0.047   0.189    498
  Planarity :  0.004   0.043    596
  Dihedral  :  5.190  28.186    491
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.42), residues: 419
  helix: -2.98 (0.84), residues: 27
  sheet:  0.55 (0.45), residues: 134
  loop : -0.29 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP H  50 
 HIS   0.003   0.001   HIS L  90 
 PHE   0.017   0.002   PHE A 429 
 TYR   0.023   0.002   TYR A 453 
 ARG   0.005   0.001   ARG L  45 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00444 (    1)
  link_NAG-ASN         : angle       2.14650 (    3)
  hydrogen bonds       : bond        0.03556 (  112)
  hydrogen bonds       : angle       6.74084 (  267)
  SS BOND              : bond        0.00599 (    6)
  SS BOND              : angle       0.96830 (   12)
  covalent geometry    : bond        0.00284 ( 3405)
  covalent geometry    : angle       0.58711 ( 4622)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: L   39 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7981 (tmtt)
REVERT: H   30 MET cc_start: 0.8745 (mmm) cc_final: 0.7966 (mmt)
REVERT: H   36 TRP cc_start: 0.8579 (m100) cc_final: 0.8226 (m100)
REVERT: H   80 MET cc_start: 0.4896 (ptm) cc_final: 0.4371 (ptm)
REVERT: H  111 GLN cc_start: 0.7769 (pm20) cc_final: 0.7281 (pt0)
REVERT: A  403 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7861 (mtp-110)
REVERT: A  473 TYR cc_start: 0.8297 (t80) cc_final: 0.7844 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.1848
  time to fit residues: 20.2169
Evaluate side-chains
  82 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 40 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 487 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.183447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.161144 restraints weight = 6261.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.165187 restraints weight = 4096.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.168120 restraints weight = 2951.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
moved from start:          0.8413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   3412  Z= 0.200
  Angle     :  0.665   8.718   4637  Z= 0.358
  Chirality :  0.049   0.202    498
  Planarity :  0.005   0.056    596
  Dihedral  :  5.872  34.958    491
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.41), residues: 419
  helix: -3.22 (0.75), residues: 29
  sheet:  0.21 (0.42), residues: 146
  loop : -0.44 (0.42), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.004   TRP H  50 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.022   0.002   PHE A 400 
 TYR   0.027   0.002   TYR A 453 
 ARG   0.016   0.001   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00356 (    1)
  link_NAG-ASN         : angle       2.52681 (    3)
  hydrogen bonds       : bond        0.03831 (  112)
  hydrogen bonds       : angle       7.04543 (  267)
  SS BOND              : bond        0.00790 (    6)
  SS BOND              : angle       1.19586 (   12)
  covalent geometry    : bond        0.00453 ( 3405)
  covalent geometry    : angle       0.66025 ( 4622)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  103 LYS cc_start: 0.8802 (tttm) cc_final: 0.8542 (tttm)
REVERT: H   36 TRP cc_start: 0.8759 (m100) cc_final: 0.8503 (m100)
REVERT: H   80 MET cc_start: 0.5193 (ptm) cc_final: 0.4866 (ptm)
REVERT: H  111 GLN cc_start: 0.7913 (pm20) cc_final: 0.7615 (pt0)
REVERT: A  473 TYR cc_start: 0.8360 (t80) cc_final: 0.7963 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1626
  time to fit residues: 15.9109
Evaluate side-chains
  75 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 11 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0470
   chunk 2 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0570
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.3196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.188629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.166363 restraints weight = 6298.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.170510 restraints weight = 4235.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.173517 restraints weight = 3082.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6705
moved from start:          0.8525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3412  Z= 0.131
  Angle     :  0.616   7.870   4637  Z= 0.326
  Chirality :  0.048   0.232    498
  Planarity :  0.005   0.056    596
  Dihedral  :  5.240  29.343    491
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.41), residues: 419
  helix: -2.71 (0.81), residues: 33
  sheet:  0.55 (0.45), residues: 134
  loop : -0.61 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP H  50 
 HIS   0.003   0.001   HIS L  90 
 PHE   0.014   0.002   PHE H  27 
 TYR   0.020   0.002   TYR A 453 
 ARG   0.013   0.001   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00332 (    1)
  link_NAG-ASN         : angle       2.21647 (    3)
  hydrogen bonds       : bond        0.03658 (  112)
  hydrogen bonds       : angle       6.70533 (  267)
  SS BOND              : bond        0.00685 (    6)
  SS BOND              : angle       0.87886 (   12)
  covalent geometry    : bond        0.00296 ( 3405)
  covalent geometry    : angle       0.61235 ( 4622)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  103 LYS cc_start: 0.8706 (tttm) cc_final: 0.8447 (tttm)
REVERT: H   36 TRP cc_start: 0.8583 (m100) cc_final: 0.8161 (m100)
REVERT: H   80 MET cc_start: 0.4889 (ptm) cc_final: 0.4412 (ptm)
REVERT: H  111 GLN cc_start: 0.7719 (pm20) cc_final: 0.7213 (pt0)
REVERT: A  403 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7809 (mtp-110)
REVERT: A  473 TYR cc_start: 0.8318 (t80) cc_final: 0.7927 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1596
  time to fit residues: 16.3892
Evaluate side-chains
  77 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0470
   chunk 32 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 26 optimal weight:    0.3980
   overall best weight:    0.3476

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.189008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.166011 restraints weight = 6231.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.170238 restraints weight = 4131.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.173266 restraints weight = 2992.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.8587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3412  Z= 0.131
  Angle     :  0.604   7.627   4637  Z= 0.322
  Chirality :  0.047   0.246    498
  Planarity :  0.005   0.054    596
  Dihedral  :  5.215  30.584    491
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.42), residues: 419
  helix: -3.02 (0.84), residues: 27
  sheet:  0.56 (0.45), residues: 134
  loop : -0.50 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP H  50 
 HIS   0.002   0.001   HIS L  90 
 PHE   0.024   0.002   PHE A 400 
 TYR   0.020   0.002   TYR A 453 
 ARG   0.013   0.001   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00338 (    1)
  link_NAG-ASN         : angle       2.26857 (    3)
  hydrogen bonds       : bond        0.03511 (  112)
  hydrogen bonds       : angle       6.69118 (  267)
  SS BOND              : bond        0.00698 (    6)
  SS BOND              : angle       0.88699 (   12)
  covalent geometry    : bond        0.00295 ( 3405)
  covalent geometry    : angle       0.60085 ( 4622)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1644.33 seconds
wall clock time: 29 minutes 32.86 seconds (1772.86 seconds total)