Starting phenix.real_space_refine
on Tue Mar  3 11:38:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d8r_27255/03_2026/8d8r_27255.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d8r_27255/03_2026/8d8r_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d8r_27255/03_2026/8d8r_27255.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d8r_27255/03_2026/8d8r_27255.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d8r_27255/03_2026/8d8r_27255.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d8r_27255/03_2026/8d8r_27255.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.82, per 1000 atoms: 0.25
  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: 0.29
  Conformation dependent library (CDL) restraints added in 91.6 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: 0.10
  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: 0.45

  Time building geometry restraints manager: 0.31 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:             4.260
  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:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.780
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.610
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG A 466 
 TYR   0.045   0.005   TYR A 423 
 PHE   0.016   0.004   PHE A 400 
 TRP   0.017   0.005   TRP H  47 
 HIS   0.002   0.001   HIS L  90 

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

*********************** 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  : 0.133 
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: 0.7565 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0722
  time to fit residues: 10.8568
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  : 0.131 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0270
   overall best weight:    0.5238

-------------------------------------------------------------------------------
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 = 0.4286 r_free = 0.4286 target = 0.194002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.171120 restraints weight = 6425.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.175780 restraints weight = 4102.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.179075 restraints weight = 2891.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.181511 restraints weight = 2181.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.183309 restraints weight = 1726.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6259
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3412  Z= 0.181
  Angle     :  0.652   5.700   4637  Z= 0.358
  Chirality :  0.045   0.133    498
  Planarity :  0.005   0.062    596
  Dihedral  :  5.168  20.400    491
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  2.22 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 are not related in a simple way.
  whole:  1.08 (0.42), residues: 419
  helix: -3.69 (0.63), residues: 28
  sheet:  0.82 (0.41), residues: 158
  loop :  1.46 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  44 
 TYR   0.018   0.002   TYR A 453 
 PHE   0.038   0.002   PHE A 400 
 TRP   0.022   0.002   TRP H  36 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 3405)
  covalent geometry    : angle       0.65170 ( 4622)
  SS BOND              : bond        0.00329 (    6)
  SS BOND              : angle       0.45021 (   12)
  hydrogen bonds       : bond        0.04226 (  112)
  hydrogen bonds       : angle       6.92281 (  267)
  link_NAG-ASN         : bond        0.00040 (    1)
  link_NAG-ASN         : angle       1.51845 (    3)

*********************** 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
  99 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8493 (m100) cc_final: 0.7879 (m100)
REVERT: A  370 ASN cc_start: 0.7004 (m-40) cc_final: 0.6793 (p0)
REVERT: A  427 ASP cc_start: 0.8004 (m-30) cc_final: 0.7533 (p0)
  outliers start: 1
  outliers final: 1
  residues processed: 98
  average time/residue: 0.0698
  time to fit residues: 8.3456
Evaluate side-chains
  86 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.3980
   chunk 26 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 29 optimal weight:    0.1980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.190127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.167403 restraints weight = 6353.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.171998 restraints weight = 4107.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.175142 restraints weight = 2907.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.177406 restraints weight = 2197.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.179095 restraints weight = 1750.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6439
moved from start:          0.5206

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= 0.172
  Angle     :  0.600   4.630   4637  Z= 0.336
  Chirality :  0.043   0.135    498
  Planarity :  0.005   0.055    596
  Dihedral  :  5.054  23.708    491
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.42), residues: 419
  helix: -3.47 (0.73), residues: 28
  sheet:  0.43 (0.38), residues: 161
  loop :  0.89 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 346 
 TYR   0.017   0.002   TYR A 473 
 PHE   0.030   0.002   PHE H  29 
 TRP   0.018   0.003   TRP A 353 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 3405)
  covalent geometry    : angle       0.59596 ( 4622)
  SS BOND              : bond        0.00351 (    6)
  SS BOND              : angle       1.31032 (   12)
  hydrogen bonds       : bond        0.04039 (  112)
  hydrogen bonds       : angle       7.02820 (  267)
  link_NAG-ASN         : bond        0.00294 (    1)
  link_NAG-ASN         : angle       1.59451 (    3)

*********************** 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
  88 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8402 (m100) cc_final: 0.8039 (m100)
REVERT: H  111 GLN cc_start: 0.7481 (pm20) cc_final: 0.7202 (pt0)
REVERT: H  118 SER cc_start: 0.5688 (t) cc_final: 0.5481 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0624
  time to fit residues: 6.8299
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  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0000
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
L  90 HIS
H  35 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.187867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.165313 restraints weight = 6364.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.169612 restraints weight = 4159.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.172691 restraints weight = 2990.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.174840 restraints weight = 2291.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.176347 restraints weight = 1853.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
moved from start:          0.6234

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= 0.169
  Angle     :  0.625  11.234   4637  Z= 0.341
  Chirality :  0.045   0.243    498
  Planarity :  0.005   0.053    596
  Dihedral  :  5.152  27.498    491
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.41), residues: 419
  helix: -3.37 (0.75), residues: 28
  sheet:  0.53 (0.40), residues: 152
  loop :  0.61 (0.43), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  54 
 TYR   0.030   0.002   TYR A 380 
 PHE   0.022   0.002   PHE H  29 
 TRP   0.015   0.002   TRP H  50 
 HIS   0.002   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 3405)
  covalent geometry    : angle       0.61929 ( 4622)
  SS BOND              : bond        0.00207 (    6)
  SS BOND              : angle       1.60036 (   12)
  hydrogen bonds       : bond        0.03554 (  112)
  hydrogen bonds       : angle       6.87492 (  267)
  link_NAG-ASN         : bond        0.00503 (    1)
  link_NAG-ASN         : angle       1.68494 (    3)

*********************** 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
  95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8499 (m100) cc_final: 0.7944 (m100)
REVERT: H   80 MET cc_start: 0.4222 (ptm) cc_final: 0.3856 (ptp)
REVERT: H  111 GLN cc_start: 0.7555 (pm20) cc_final: 0.7291 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0645
  time to fit residues: 7.5521
Evaluate side-chains
  78 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    0.0670
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0870
   chunk 31 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.4496

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.189637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.167245 restraints weight = 6276.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.171688 restraints weight = 4054.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.174792 restraints weight = 2871.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.177096 restraints weight = 2176.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.178734 restraints weight = 1728.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6526
moved from start:          0.6740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3412  Z= 0.154
  Angle     :  0.698  15.847   4637  Z= 0.374
  Chirality :  0.048   0.371    498
  Planarity :  0.005   0.046    596
  Dihedral  :  5.146  30.478    491
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.42), residues: 419
  helix: -3.28 (0.78), residues: 28
  sheet:  0.79 (0.43), residues: 134
  loop :  0.33 (0.41), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  54 
 TYR   0.026   0.002   TYR A 380 
 PHE   0.030   0.002   PHE H  29 
 TRP   0.027   0.003   TRP L  96 
 HIS   0.006   0.002   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3405)
  covalent geometry    : angle       0.66274 ( 4622)
  SS BOND              : bond        0.00284 (    6)
  SS BOND              : angle       3.88627 (   12)
  hydrogen bonds       : bond        0.03707 (  112)
  hydrogen bonds       : angle       6.53634 (  267)
  link_NAG-ASN         : bond        0.01070 (    1)
  link_NAG-ASN         : angle       4.01761 (    3)

*********************** 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
  93 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: L   91 TYR cc_start: 0.7366 (m-10) cc_final: 0.6656 (m-10)
REVERT: H   36 TRP cc_start: 0.8468 (m100) cc_final: 0.7873 (m100)
REVERT: H   38 ARG cc_start: 0.8613 (tmm-80) cc_final: 0.8252 (tmm-80)
REVERT: H   80 MET cc_start: 0.4187 (ptm) cc_final: 0.3832 (ptp)
REVERT: H  111 GLN cc_start: 0.7628 (pm20) cc_final: 0.7350 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0791
  time to fit residues: 8.7766
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  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0470
   chunk 17 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0170
   chunk 3 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 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 = 0.4236 r_free = 0.4236 target = 0.190585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.168177 restraints weight = 6392.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.172702 restraints weight = 4080.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.175805 restraints weight = 2881.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.177989 restraints weight = 2185.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.179619 restraints weight = 1749.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6555
moved from start:          0.7218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3412  Z= 0.140
  Angle     :  0.685  15.187   4637  Z= 0.364
  Chirality :  0.048   0.325    498
  Planarity :  0.004   0.040    596
  Dihedral  :  5.099  27.331    491
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.42), residues: 419
  helix: -3.03 (0.81), residues: 28
  sheet:  0.89 (0.45), residues: 129
  loop :  0.24 (0.41), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  54 
 TYR   0.027   0.002   TYR A 380 
 PHE   0.033   0.002   PHE A 400 
 TRP   0.022   0.002   TRP H  50 
 HIS   0.003   0.002   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3405)
  covalent geometry    : angle       0.64732 ( 4622)
  SS BOND              : bond        0.00684 (    6)
  SS BOND              : angle       4.27023 (   12)
  hydrogen bonds       : bond        0.03558 (  112)
  hydrogen bonds       : angle       6.55792 (  267)
  link_NAG-ASN         : bond        0.00718 (    1)
  link_NAG-ASN         : angle       2.63077 (    3)

*********************** 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
  90 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: H   36 TRP cc_start: 0.8488 (m100) cc_final: 0.7992 (m100)
REVERT: H   80 MET cc_start: 0.4388 (ptm) cc_final: 0.4021 (ptp)
REVERT: H  111 GLN cc_start: 0.7649 (pm20) cc_final: 0.7374 (pt0)
REVERT: A  402 ILE cc_start: 0.8628 (pt) cc_final: 0.8417 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0818
  time to fit residues: 8.7593
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  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.3980
   chunk 19 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0570
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0040
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.3510

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 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 = 0.4266 r_free = 0.4266 target = 0.193162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.171165 restraints weight = 6643.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.175337 restraints weight = 4400.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.178205 restraints weight = 3179.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.180113 restraints weight = 2455.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.181818 restraints weight = 2012.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.7535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3412  Z= 0.132
  Angle     :  0.663  13.533   4637  Z= 0.349
  Chirality :  0.047   0.274    498
  Planarity :  0.004   0.040    596
  Dihedral  :  4.739  26.706    491
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.42), residues: 419
  helix: -2.99 (0.81), residues: 28
  sheet:  1.09 (0.48), residues: 117
  loop :  0.13 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  45 
 TYR   0.020   0.002   TYR A 495 
 PHE   0.015   0.002   PHE A 400 
 TRP   0.021   0.002   TRP H  50 
 HIS   0.004   0.002   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3405)
  covalent geometry    : angle       0.63159 ( 4622)
  SS BOND              : bond        0.00337 (    6)
  SS BOND              : angle       3.85451 (   12)
  hydrogen bonds       : bond        0.03472 (  112)
  hydrogen bonds       : angle       6.36414 (  267)
  link_NAG-ASN         : bond        0.00556 (    1)
  link_NAG-ASN         : angle       2.38906 (    3)

*********************** 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
  91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   91 TYR cc_start: 0.7416 (m-10) cc_final: 0.6693 (m-10)
REVERT: H   36 TRP cc_start: 0.8467 (m100) cc_final: 0.8134 (m100)
REVERT: H   52 ILE cc_start: 0.7708 (mm) cc_final: 0.7472 (mm)
REVERT: H   67 VAL cc_start: 0.8672 (p) cc_final: 0.8467 (p)
REVERT: H   80 MET cc_start: 0.4269 (ptm) cc_final: 0.3929 (ptp)
REVERT: H  111 GLN cc_start: 0.7729 (pm20) cc_final: 0.7418 (pt0)
REVERT: A  403 ARG cc_start: 0.7878 (mtp85) cc_final: 0.7664 (mtp85)
REVERT: A  473 TYR cc_start: 0.8296 (t80) cc_final: 0.7957 (t80)
REVERT: A  516 GLU cc_start: 0.5969 (tt0) cc_final: 0.5758 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.0657
  time to fit residues: 7.3568
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  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    0.0870
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.5560

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 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 = 0.4215 r_free = 0.4215 target = 0.188457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.165885 restraints weight = 6790.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.169910 restraints weight = 4551.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.173001 restraints weight = 3374.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.174909 restraints weight = 2623.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.176584 restraints weight = 2156.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6643
moved from start:          0.7933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3412  Z= 0.166
  Angle     :  0.690  12.576   4637  Z= 0.370
  Chirality :  0.049   0.289    498
  Planarity :  0.004   0.039    596
  Dihedral  :  5.277  27.370    491
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.42), residues: 419
  helix: -3.00 (0.81), residues: 28
  sheet:  0.93 (0.48), residues: 119
  loop : -0.06 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  45 
 TYR   0.024   0.002   TYR A 423 
 PHE   0.010   0.002   PHE H  29 
 TRP   0.031   0.003   TRP H  50 
 HIS   0.002   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3405)
  covalent geometry    : angle       0.65774 ( 4622)
  SS BOND              : bond        0.00623 (    6)
  SS BOND              : angle       4.06089 (   12)
  hydrogen bonds       : bond        0.03792 (  112)
  hydrogen bonds       : angle       6.68526 (  267)
  link_NAG-ASN         : bond        0.00733 (    1)
  link_NAG-ASN         : angle       1.96922 (    3)

*********************** 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
  93 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   91 TYR cc_start: 0.7245 (m-10) cc_final: 0.6726 (m-10)
REVERT: L  103 LYS cc_start: 0.8792 (tttt) cc_final: 0.8480 (tttm)
REVERT: H   36 TRP cc_start: 0.8533 (m100) cc_final: 0.8069 (m100)
REVERT: H   80 MET cc_start: 0.4443 (ptm) cc_final: 0.4151 (ptp)
REVERT: H  111 GLN cc_start: 0.7950 (pm20) cc_final: 0.7314 (pt0)
REVERT: A  473 TYR cc_start: 0.8353 (t80) cc_final: 0.7927 (t80)
REVERT: A  516 GLU cc_start: 0.6086 (tt0) cc_final: 0.5668 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0736
  time to fit residues: 8.1849
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  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 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 = 0.4204 r_free = 0.4204 target = 0.186543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.164245 restraints weight = 6543.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.168339 restraints weight = 4324.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.171285 restraints weight = 3132.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.173166 restraints weight = 2434.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.174771 restraints weight = 2010.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6707
moved from start:          0.8397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   3412  Z= 0.189
  Angle     :  0.719  12.357   4637  Z= 0.384
  Chirality :  0.050   0.294    498
  Planarity :  0.004   0.039    596
  Dihedral  :  6.075  41.129    491
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 are not related in a simple way.
  whole: -0.39 (0.42), residues: 419
  helix: -2.96 (0.76), residues: 34
  sheet:  0.74 (0.47), residues: 129
  loop : -0.36 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  45 
 TYR   0.030   0.002   TYR A 453 
 PHE   0.023   0.002   PHE A 400 
 TRP   0.036   0.003   TRP H  50 
 HIS   0.002   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 3405)
  covalent geometry    : angle       0.68876 ( 4622)
  SS BOND              : bond        0.00295 (    6)
  SS BOND              : angle       3.97070 (   12)
  hydrogen bonds       : bond        0.03869 (  112)
  hydrogen bonds       : angle       6.86910 (  267)
  link_NAG-ASN         : bond        0.00504 (    1)
  link_NAG-ASN         : angle       2.30743 (    3)

*********************** 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
  94 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  103 LYS cc_start: 0.8828 (tttt) cc_final: 0.8446 (tttm)
REVERT: H   36 TRP cc_start: 0.8623 (m100) cc_final: 0.8094 (m100)
REVERT: H   80 MET cc_start: 0.4600 (ptm) cc_final: 0.4284 (ptp)
REVERT: H   89 VAL cc_start: 0.7510 (t) cc_final: 0.7291 (t)
REVERT: H  111 GLN cc_start: 0.7945 (pm20) cc_final: 0.7500 (pt0)
REVERT: A  473 TYR cc_start: 0.8441 (t80) cc_final: 0.8044 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.0745
  time to fit residues: 8.4449
Evaluate side-chains
  80 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:    0.1980
   chunk 1 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0770
   chunk 31 optimal weight:    0.0030
   chunk 15 optimal weight:    0.0000
   chunk 7 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0570
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.0670

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
H  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.195504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.173712 restraints weight = 6314.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.177954 restraints weight = 4139.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.181165 restraints weight = 2958.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.183347 restraints weight = 2220.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.184968 restraints weight = 1756.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6476
moved from start:          0.8531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   3412  Z= 0.111
  Angle     :  0.657  10.445   4637  Z= 0.344
  Chirality :  0.048   0.293    498
  Planarity :  0.004   0.042    596
  Dihedral  :  4.761  27.245    491
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.42), residues: 419
  helix: -2.94 (0.84), residues: 28
  sheet:  1.19 (0.49), residues: 119
  loop : -0.14 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 509 
 TYR   0.024   0.002   TYR H  59 
 PHE   0.013   0.001   PHE A 429 
 TRP   0.009   0.002   TRP A 353 
 HIS   0.004   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 3405)
  covalent geometry    : angle       0.62732 ( 4622)
  SS BOND              : bond        0.00140 (    6)
  SS BOND              : angle       3.67715 (   12)
  hydrogen bonds       : bond        0.03532 (  112)
  hydrogen bonds       : angle       6.24443 (  267)
  link_NAG-ASN         : bond        0.00243 (    1)
  link_NAG-ASN         : angle       2.43538 (    3)

********************** 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
  91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  103 LYS cc_start: 0.8769 (tttt) cc_final: 0.8492 (tttm)
REVERT: H   36 TRP cc_start: 0.8238 (m100) cc_final: 0.8020 (m100)
REVERT: H   47 TRP cc_start: 0.8219 (t60) cc_final: 0.7970 (t60)
REVERT: H   52 ILE cc_start: 0.8012 (mm) cc_final: 0.7710 (mm)
REVERT: H   80 MET cc_start: 0.4252 (ptm) cc_final: 0.3950 (ptp)
REVERT: H  111 GLN cc_start: 0.7708 (pm20) cc_final: 0.6995 (pt0)
REVERT: A  473 TYR cc_start: 0.8337 (t80) cc_final: 0.8054 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0817
  time to fit residues: 8.6877
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  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 11 optimal weight:    0.4980
   chunk 16 optimal weight:    0.3980
   chunk 36 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   overall best weight:    0.3580

-------------------------------------------------------------------------------
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 = 0.4252 r_free = 0.4252 target = 0.191715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.168557 restraints weight = 6362.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.172779 restraints weight = 4242.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.175889 restraints weight = 3087.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.178150 restraints weight = 2380.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.179450 restraints weight = 1919.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6595
moved from start:          0.8626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3412  Z= 0.132
  Angle     :  0.661  10.747   4637  Z= 0.347
  Chirality :  0.048   0.253    498
  Planarity :  0.005   0.063    596
  Dihedral  :  5.082  29.397    491
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.42), residues: 419
  helix: -2.86 (0.82), residues: 34
  sheet:  1.13 (0.48), residues: 119
  loop : -0.22 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 346 
 TYR   0.021   0.002   TYR A 423 
 PHE   0.013   0.001   PHE L  98 
 TRP   0.016   0.002   TRP H  50 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3405)
  covalent geometry    : angle       0.63143 ( 4622)
  SS BOND              : bond        0.00222 (    6)
  SS BOND              : angle       3.70629 (   12)
  hydrogen bonds       : bond        0.03534 (  112)
  hydrogen bonds       : angle       6.44054 (  267)
  link_NAG-ASN         : bond        0.00389 (    1)
  link_NAG-ASN         : angle       2.40862 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 921.46 seconds
wall clock time: 16 minutes 29.48 seconds (989.48 seconds total)