Starting phenix.real_space_refine
on Wed Jul 23 15:40:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr0_34041/07_2025/7yr0_34041.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr0_34041/07_2025/7yr0_34041.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yr0_34041/07_2025/7yr0_34041.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr0_34041/07_2025/7yr0_34041.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr0_34041/07_2025/7yr0_34041.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr0_34041/07_2025/7yr0_34041.cif"
  }
  resolution = 3.98
  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=  -0.001 sd=   0.044
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      15      5.16       5
     C    2149      2.51       5
     N     571      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3383
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1560
          Classifications: {'peptide': 196}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 183}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "C"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 959
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
    Chain: "B"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 815
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 49
          Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 3.34, per 1000 atoms: 0.99
  Number of scatterers: 3383
  At special positions: 0
  Unit cell: (73.83, 85.6, 81.32, 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      15     16.00
     O     648      8.00
     N     571      7.00
     C    2149      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    BETA1-6
      " NAG D   1 " - " FUC D   4 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG D   1 " - " ASN A 343 "
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 378.6 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 8 sheets defined
      6.3% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 3.995A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   PHE A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 337 through 342'
    Processing helix  chain 'A' and resid 365 through 370
      removed outlier: 3.799A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'C' and resid 61 through 65
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.310A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
      removed outlier: 3.597A  pdb=" N   TYR A 453 " --> pdb=" O   GLN A 493 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 51
      removed outlier: 3.890A  pdb=" N   GLY C  33 " --> pdb=" O   ASP C  99 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ASN C 116 " --> pdb=" O   ARG C  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 49 through 51
      removed outlier: 3.890A  pdb=" N   GLY C  33 " --> pdb=" O   ASP C  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11
      removed outlier: 3.697A  pdb=" N   LEU B  11 " --> pdb=" O   LYS B 103 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 22
      removed outlier: 3.763A  pdb=" N   ASP B  71 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 47
      removed outlier: 4.117A  pdb=" N   THR B  97 " --> pdb=" O   GLN B  91 " (cutoff:3.500A)

    82 hydrogen bonds defined for protein.
    189 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: 0.76

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1073
        1.35 -     1.46: 942
        1.46 -     1.58: 1439
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 3472
  Sorted by residual:
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.547 -0.028 2.00e-02 2.50e+03 1.96e+00
  bond pdb=" C2  NAG D   2 "
       pdb=" N2  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.439  1.464 -0.025 2.00e-02 2.50e+03 1.58e+00
  bond pdb=" CA  GLY A 381 "
       pdb=" C   GLY A 381 "
    ideal  model  delta    sigma   weight residual
    1.512  1.523 -0.011 8.70e-03 1.32e+04 1.56e+00
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.38e+00
  bond pdb=" C5  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.36e+00
  ... (remaining 3467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 4462
        1.26 -     2.51: 185
        2.51 -     3.77: 51
        3.77 -     5.02: 17
        5.02 -     6.28: 5
  Bond angle restraints: 4720
  Sorted by residual:
  angle pdb=" N   ILE A 402 "
        pdb=" CA  ILE A 402 "
        pdb=" C   ILE A 402 "
      ideal   model   delta    sigma   weight residual
     108.53  111.81   -3.28 1.22e+00 6.72e-01 7.23e+00
  angle pdb=" C   GLU C  82 "
        pdb=" CA  GLU C  82 "
        pdb=" CB  GLU C  82 "
      ideal   model   delta    sigma   weight residual
     110.42  115.40   -4.98 1.99e+00 2.53e-01 6.25e+00
  angle pdb=" C   GLU B  80 "
        pdb=" CA  GLU B  80 "
        pdb=" CB  GLU B  80 "
      ideal   model   delta    sigma   weight residual
     109.26  112.83   -3.57 1.47e+00 4.63e-01 5.91e+00
  angle pdb=" C   MET C  48 "
        pdb=" N   GLY C  49 "
        pdb=" CA  GLY C  49 "
      ideal   model   delta    sigma   weight residual
     121.46  119.21    2.25 9.50e-01 1.11e+00 5.63e+00
  angle pdb=" N   GLY C  49 "
        pdb=" CA  GLY C  49 "
        pdb=" C   GLY C  49 "
      ideal   model   delta    sigma   weight residual
     110.90  114.36   -3.46 1.53e+00 4.27e-01 5.12e+00
  ... (remaining 4715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.07: 1915
       22.07 -    44.14: 136
       44.14 -    66.21: 11
       66.21 -    88.28: 9
       88.28 -   110.35: 5
  Dihedral angle restraints: 2076
    sinusoidal: 851
      harmonic: 1225
  Sorted by residual:
  dihedral pdb=" CA  SER B   7 "
           pdb=" C   SER B   7 "
           pdb=" N   PRO B   8 "
           pdb=" CA  PRO B   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.07   25.93     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.67   38.33     1      1.00e+01 1.00e-02 2.07e+01
  dihedral pdb=" CA  TYR C  80 "
           pdb=" C   TYR C  80 "
           pdb=" N   MET C  81 "
           pdb=" CA  MET C  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.93   22.07     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 2073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 448
       0.066 -    0.133: 61
       0.133 -    0.199: 4
       0.199 -    0.265: 0
       0.265 -    0.331: 2
  Chirality restraints: 515
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" C2  NAG D   2 "
            pdb=" C1  NAG D   2 "
            pdb=" C3  NAG D   2 "
            pdb=" N2  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.31   -0.19 2.00e-01 2.50e+01 8.59e-01
  ... (remaining 512 not shown)

  Planarity restraints: 606
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B   7 "   -0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO B   8 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B   8 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B   8 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP C  47 "    0.006 2.00e-02 2.50e+03   1.16e-02 1.35e+00
        pdb=" C   TRP C  47 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   TRP C  47 "    0.008 2.00e-02 2.50e+03
        pdb=" N   MET C  48 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  47 "    0.009 2.00e-02 2.50e+03   7.14e-03 1.27e+00
        pdb=" CG  TRP C  47 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  47 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  47 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  47 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  47 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  47 "    0.001 2.00e-02 2.50e+03
  ... (remaining 603 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 130
        2.71 -     3.26: 3238
        3.26 -     3.81: 5061
        3.81 -     4.35: 6100
        4.35 -     4.90: 10380
  Nonbonded interactions: 24909
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  69 "
            pdb=" OE2 GLU C  82 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   VAL B   3 "
            pdb=" OG  SER B  26 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OG  SER C  35 "
            pdb=" OD2 ASP C  99 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" NH1 ARG C  87 "
            pdb=" OD1 ASP C  89 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   ALA A 419 "
            pdb=" NZ  LYS A 424 "
     model   vdw
     2.259 3.120
  ... (remaining 24904 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:             3.440
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.230
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3481  Z= 0.154
  Angle     :  0.708   8.519   4742  Z= 0.353
  Chirality :  0.049   0.331    515
  Planarity :  0.004   0.034    605
  Dihedral  : 15.968 110.350   1287
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.43), residues: 421
  helix: -0.21 (3.10), residues: 6
  sheet:  0.50 (0.59), residues: 92
  loop : -1.86 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  47 
 HIS   0.002   0.001   HIS B  92 
 PHE   0.017   0.001   PHE C  29 
 TYR   0.012   0.001   TYR B  50 
 ARG   0.003   0.000   ARG B  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02652 (    1)
  link_NAG-ASN         : angle       6.73296 (    3)
  link_BETA1-4         : bond        0.00448 (    2)
  link_BETA1-4         : angle       2.64261 (    6)
  hydrogen bonds       : bond        0.13084 (   71)
  hydrogen bonds       : angle       5.73812 (  189)
  link_BETA1-6         : bond        0.00327 (    1)
  link_BETA1-6         : angle       1.33975 (    3)
  SS BOND              : bond        0.00316 (    5)
  SS BOND              : angle       0.74826 (   10)
  covalent geometry    : bond        0.00311 ( 3472)
  covalent geometry    : angle       0.68081 ( 4720)

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

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.374 
Fit side-chains
REVERT: C   80 TYR cc_start: 0.8049 (m-80) cc_final: 0.7822 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1762
  time to fit residues: 15.9353
Evaluate side-chains
  57 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 12 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.121880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.095506 restraints weight = 8020.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.097856 restraints weight = 5535.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.099512 restraints weight = 4356.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3481  Z= 0.207
  Angle     :  0.734   9.632   4742  Z= 0.355
  Chirality :  0.048   0.235    515
  Planarity :  0.004   0.037    605
  Dihedral  : 10.015  63.953    552
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.98 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 13.76 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.42), residues: 421
  helix: -2.60 (1.22), residues: 18
  sheet:  0.24 (0.58), residues: 98
  loop : -1.89 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.004   0.002   HIS B  92 
 PHE   0.012   0.002   PHE C  29 
 TYR   0.026   0.002   TYR B  50 
 ARG   0.010   0.001   ARG B  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02250 (    1)
  link_NAG-ASN         : angle       7.94327 (    3)
  link_BETA1-4         : bond        0.00301 (    2)
  link_BETA1-4         : angle       2.37401 (    6)
  hydrogen bonds       : bond        0.03403 (   71)
  hydrogen bonds       : angle       5.83981 (  189)
  link_BETA1-6         : bond        0.00441 (    1)
  link_BETA1-6         : angle       1.19753 (    3)
  SS BOND              : bond        0.00495 (    5)
  SS BOND              : angle       0.77506 (   10)
  covalent geometry    : bond        0.00476 ( 3472)
  covalent geometry    : angle       0.70158 ( 4720)

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

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASN cc_start: 0.8082 (m110) cc_final: 0.7825 (p0)
  outliers start: 5
  outliers final: 4
  residues processed: 66
  average time/residue: 0.1683
  time to fit residues: 13.4357
Evaluate side-chains
  62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 33 optimal weight:    0.2980
   chunk 35 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0030
   chunk 16 optimal weight:    0.8980
   chunk 3 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0670
   overall best weight:    0.2928

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.125433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.099386 restraints weight = 7840.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.101924 restraints weight = 5278.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.103750 restraints weight = 4101.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3481  Z= 0.113
  Angle     :  0.686   9.755   4742  Z= 0.318
  Chirality :  0.047   0.274    515
  Planarity :  0.004   0.035    605
  Dihedral  :  7.473  58.842    552
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.89 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.61 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.42), residues: 421
  helix: -2.03 (1.69), residues: 12
  sheet:  0.59 (0.59), residues: 92
  loop : -1.84 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.017   0.001   PHE C  29 
 TYR   0.022   0.001   TYR B  50 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02584 (    1)
  link_NAG-ASN         : angle       8.14965 (    3)
  link_BETA1-4         : bond        0.00804 (    2)
  link_BETA1-4         : angle       2.76660 (    6)
  hydrogen bonds       : bond        0.02888 (   71)
  hydrogen bonds       : angle       5.39350 (  189)
  link_BETA1-6         : bond        0.00490 (    1)
  link_BETA1-6         : angle       0.79008 (    3)
  SS BOND              : bond        0.00331 (    5)
  SS BOND              : angle       0.79586 (   10)
  covalent geometry    : bond        0.00251 ( 3472)
  covalent geometry    : angle       0.64719 ( 4720)

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

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASN cc_start: 0.7990 (m110) cc_final: 0.7785 (p0)
REVERT: C   80 TYR cc_start: 0.8058 (m-80) cc_final: 0.7818 (m-80)
REVERT: C   82 GLU cc_start: 0.5895 (pp20) cc_final: 0.5382 (tm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 72
  average time/residue: 0.1766
  time to fit residues: 15.2413
Evaluate side-chains
  61 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0020
   chunk 7 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 12 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6788

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.124411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.098392 restraints weight = 7988.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.100908 restraints weight = 5471.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.102544 restraints weight = 4253.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3481  Z= 0.126
  Angle     :  0.660   9.537   4742  Z= 0.313
  Chirality :  0.046   0.252    515
  Planarity :  0.003   0.036    605
  Dihedral  :  6.983  58.989    552
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.79 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.54 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.41), residues: 421
  helix: -1.79 (1.34), residues: 20
  sheet:  0.78 (0.60), residues: 90
  loop : -1.91 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.016   0.001   PHE C  29 
 TYR   0.017   0.001   TYR A 501 
 ARG   0.002   0.000   ARG C  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02730 (    1)
  link_NAG-ASN         : angle       7.06065 (    3)
  link_BETA1-4         : bond        0.00360 (    2)
  link_BETA1-4         : angle       2.65230 (    6)
  hydrogen bonds       : bond        0.02964 (   71)
  hydrogen bonds       : angle       5.43534 (  189)
  link_BETA1-6         : bond        0.00441 (    1)
  link_BETA1-6         : angle       1.21196 (    3)
  SS BOND              : bond        0.00332 (    5)
  SS BOND              : angle       0.80384 (   10)
  covalent geometry    : bond        0.00290 ( 3472)
  covalent geometry    : angle       0.62861 ( 4720)

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

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: C   80 TYR cc_start: 0.8058 (m-80) cc_final: 0.7807 (m-80)
REVERT: C   82 GLU cc_start: 0.5827 (pp20) cc_final: 0.5349 (tm-30)
  outliers start: 7
  outliers final: 5
  residues processed: 68
  average time/residue: 0.1690
  time to fit residues: 13.8641
Evaluate side-chains
  62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 34 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 15 optimal weight:    0.2980
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.124491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.098457 restraints weight = 8111.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.100929 restraints weight = 5490.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.102604 restraints weight = 4294.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3481  Z= 0.136
  Angle     :  0.679   9.582   4742  Z= 0.323
  Chirality :  0.047   0.248    515
  Planarity :  0.003   0.033    605
  Dihedral  :  6.681  57.696    552
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.60 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.51 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.42), residues: 421
  helix: -1.85 (1.84), residues: 12
  sheet:  0.80 (0.60), residues: 90
  loop : -1.78 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.014   0.003   HIS A 505 
 PHE   0.007   0.001   PHE A 400 
 TYR   0.019   0.001   TYR B  50 
 ARG   0.001   0.000   ARG C  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02712 (    1)
  link_NAG-ASN         : angle       7.26105 (    3)
  link_BETA1-4         : bond        0.00601 (    2)
  link_BETA1-4         : angle       2.89062 (    6)
  hydrogen bonds       : bond        0.02824 (   71)
  hydrogen bonds       : angle       5.52816 (  189)
  link_BETA1-6         : bond        0.00193 (    1)
  link_BETA1-6         : angle       1.35631 (    3)
  SS BOND              : bond        0.00362 (    5)
  SS BOND              : angle       0.82553 (   10)
  covalent geometry    : bond        0.00313 ( 3472)
  covalent geometry    : angle       0.64523 ( 4720)

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

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5935 (pp20) cc_final: 0.5532 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 67
  average time/residue: 0.1732
  time to fit residues: 13.9595
Evaluate side-chains
  64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:    0.0670
   chunk 0 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6720

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.125267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.100859 restraints weight = 7967.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.103349 restraints weight = 5304.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.105034 restraints weight = 4090.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3481  Z= 0.127
  Angle     :  0.669   9.496   4742  Z= 0.321
  Chirality :  0.047   0.261    515
  Planarity :  0.003   0.035    605
  Dihedral  :  6.618  57.705    552
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 19.66 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.60 (0.42), residues: 421
  helix: -1.97 (1.77), residues: 12
  sheet:  0.80 (0.60), residues: 90
  loop : -1.74 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 436 
 HIS   0.001   0.001   HIS A 339 
 PHE   0.008   0.001   PHE A 342 
 TYR   0.022   0.001   TYR B  50 
 ARG   0.001   0.000   ARG C  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03342 (    1)
  link_NAG-ASN         : angle       6.19731 (    3)
  link_BETA1-4         : bond        0.00574 (    2)
  link_BETA1-4         : angle       3.36835 (    6)
  hydrogen bonds       : bond        0.02807 (   71)
  hydrogen bonds       : angle       5.42827 (  189)
  link_BETA1-6         : bond        0.00266 (    1)
  link_BETA1-6         : angle       1.14561 (    3)
  SS BOND              : bond        0.00344 (    5)
  SS BOND              : angle       0.84363 (   10)
  covalent geometry    : bond        0.00289 ( 3472)
  covalent geometry    : angle       0.63888 ( 4720)

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

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5778 (pp20) cc_final: 0.5439 (tm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 68
  average time/residue: 0.1710
  time to fit residues: 14.0152
Evaluate side-chains
  62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0060
   chunk 17 optimal weight:    3.9990
   chunk 30 optimal weight:    0.2980
   chunk 13 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.0600

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.123845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.099225 restraints weight = 7853.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.101583 restraints weight = 5310.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.103231 restraints weight = 4133.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3481  Z= 0.162
  Angle     :  0.693   9.566   4742  Z= 0.338
  Chirality :  0.047   0.243    515
  Planarity :  0.004   0.032    605
  Dihedral  :  6.910  58.900    552
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.66 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.41), residues: 421
  helix: -2.08 (1.25), residues: 20
  sheet:  0.63 (0.59), residues: 93
  loop : -1.93 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.019   0.004   HIS A 505 
 PHE   0.010   0.001   PHE A 377 
 TYR   0.019   0.002   TYR B  50 
 ARG   0.002   0.000   ARG C  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03226 (    1)
  link_NAG-ASN         : angle       6.32468 (    3)
  link_BETA1-4         : bond        0.00363 (    2)
  link_BETA1-4         : angle       2.81789 (    6)
  hydrogen bonds       : bond        0.02935 (   71)
  hydrogen bonds       : angle       5.60757 (  189)
  link_BETA1-6         : bond        0.00312 (    1)
  link_BETA1-6         : angle       1.34086 (    3)
  SS BOND              : bond        0.00403 (    5)
  SS BOND              : angle       0.90317 (   10)
  covalent geometry    : bond        0.00372 ( 3472)
  covalent geometry    : angle       0.66648 ( 4720)

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

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5912 (pp20) cc_final: 0.5533 (tm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 69
  average time/residue: 0.1714
  time to fit residues: 14.3250
Evaluate side-chains
  64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0670
   chunk 1 optimal weight:    0.3980
   chunk 17 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 = 0.3752 r_free = 0.3752 target = 0.125652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.100523 restraints weight = 7900.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.103097 restraints weight = 5239.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.104873 restraints weight = 3996.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3481  Z= 0.122
  Angle     :  0.697   9.529   4742  Z= 0.336
  Chirality :  0.047   0.269    515
  Planarity :  0.003   0.035    605
  Dihedral  :  6.377  57.596    552
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.55 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.66 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.42), residues: 421
  helix: -2.08 (1.72), residues: 12
  sheet:  0.55 (0.58), residues: 95
  loop : -1.76 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.001   0.001   HIS B  92 
 PHE   0.007   0.001   PHE A 377 
 TYR   0.020   0.001   TYR B  50 
 ARG   0.003   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03649 (    1)
  link_NAG-ASN         : angle       5.96152 (    3)
  link_BETA1-4         : bond        0.00735 (    2)
  link_BETA1-4         : angle       3.47799 (    6)
  hydrogen bonds       : bond        0.02782 (   71)
  hydrogen bonds       : angle       5.44349 (  189)
  link_BETA1-6         : bond        0.00031 (    1)
  link_BETA1-6         : angle       1.33645 (    3)
  SS BOND              : bond        0.00329 (    5)
  SS BOND              : angle       0.85661 (   10)
  covalent geometry    : bond        0.00275 ( 3472)
  covalent geometry    : angle       0.66937 ( 4720)

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

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A  490 PHE cc_start: 0.6234 (OUTLIER) cc_final: 0.5847 (t80)
REVERT: C   82 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5562 (tm-30)
  outliers start: 13
  outliers final: 9
  residues processed: 68
  average time/residue: 0.1729
  time to fit residues: 14.3570
Evaluate side-chains
  71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  490 PHE
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0040
   chunk 14 optimal weight:    0.0010
   chunk 19 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 9 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.2998

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.127279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.102463 restraints weight = 7824.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.105138 restraints weight = 5078.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.106725 restraints weight = 3851.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3481  Z= 0.111
  Angle     :  0.674   9.612   4742  Z= 0.321
  Chirality :  0.046   0.251    515
  Planarity :  0.003   0.032    605
  Dihedral  :  6.141  57.258    552
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.84 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 19.66 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.61 (0.42), residues: 421
  helix: -2.28 (1.62), residues: 12
  sheet:  0.63 (0.59), residues: 95
  loop : -1.71 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 436 
 HIS   0.001   0.001   HIS B  92 
 PHE   0.006   0.001   PHE A 377 
 TYR   0.019   0.001   TYR B  50 
 ARG   0.002   0.000   ARG B  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03088 (    1)
  link_NAG-ASN         : angle       6.25513 (    3)
  link_BETA1-4         : bond        0.00566 (    2)
  link_BETA1-4         : angle       3.04501 (    6)
  hydrogen bonds       : bond        0.02644 (   71)
  hydrogen bonds       : angle       5.27029 (  189)
  link_BETA1-6         : bond        0.00373 (    1)
  link_BETA1-6         : angle       1.19827 (    3)
  SS BOND              : bond        0.00281 (    5)
  SS BOND              : angle       0.83960 (   10)
  covalent geometry    : bond        0.00249 ( 3472)
  covalent geometry    : angle       0.64567 ( 4720)

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

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  490 PHE cc_start: 0.6237 (OUTLIER) cc_final: 0.5836 (t80)
REVERT: C   82 GLU cc_start: 0.5920 (OUTLIER) cc_final: 0.5540 (tm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 69
  average time/residue: 0.1706
  time to fit residues: 14.1966
Evaluate side-chains
  67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  490 PHE
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0060
   chunk 37 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 39 optimal weight:    0.1980
   chunk 21 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 30 optimal weight:    0.1980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.127101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102301 restraints weight = 7822.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.104904 restraints weight = 5094.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.106487 restraints weight = 3872.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3481  Z= 0.115
  Angle     :  0.691   9.613   4742  Z= 0.327
  Chirality :  0.045   0.246    515
  Planarity :  0.003   0.035    605
  Dihedral  :  6.131  57.318    552
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 19.94 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.42), residues: 421
  helix: -2.19 (1.68), residues: 12
  sheet:  0.58 (0.60), residues: 95
  loop : -1.72 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.001   0.001   HIS A 339 
 PHE   0.007   0.001   PHE A 342 
 TYR   0.019   0.001   TYR B  50 
 ARG   0.002   0.000   ARG C  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02817 (    1)
  link_NAG-ASN         : angle       6.46041 (    3)
  link_BETA1-4         : bond        0.00500 (    2)
  link_BETA1-4         : angle       2.88994 (    6)
  hydrogen bonds       : bond        0.02723 (   71)
  hydrogen bonds       : angle       5.28830 (  189)
  link_BETA1-6         : bond        0.00213 (    1)
  link_BETA1-6         : angle       1.28155 (    3)
  SS BOND              : bond        0.00297 (    5)
  SS BOND              : angle       0.82843 (   10)
  covalent geometry    : bond        0.00268 ( 3472)
  covalent geometry    : angle       0.66316 ( 4720)

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

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: A  490 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5826 (t80)
REVERT: C   82 GLU cc_start: 0.5907 (OUTLIER) cc_final: 0.5544 (tm-30)
REVERT: C   94 TYR cc_start: 0.7855 (m-80) cc_final: 0.7467 (m-80)
  outliers start: 9
  outliers final: 6
  residues processed: 64
  average time/residue: 0.1655
  time to fit residues: 12.8862
Evaluate side-chains
  63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  490 PHE
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3736 r_free = 0.3736 target = 0.124579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.099333 restraints weight = 7960.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.101842 restraints weight = 5276.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.103583 restraints weight = 4061.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3481  Z= 0.165
  Angle     :  0.718   9.627   4742  Z= 0.348
  Chirality :  0.046   0.231    515
  Planarity :  0.004   0.032    605
  Dihedral  :  6.554  58.617    552
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.74 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.35 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.41), residues: 421
  helix: -2.27 (1.20), residues: 20
  sheet:  0.60 (0.60), residues: 93
  loop : -1.84 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  47 
 HIS   0.003   0.001   HIS A 339 
 PHE   0.009   0.001   PHE C  29 
 TYR   0.021   0.001   TYR B  50 
 ARG   0.002   0.000   ARG C  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02692 (    1)
  link_NAG-ASN         : angle       6.49763 (    3)
  link_BETA1-4         : bond        0.00276 (    2)
  link_BETA1-4         : angle       2.33935 (    6)
  hydrogen bonds       : bond        0.02977 (   71)
  hydrogen bonds       : angle       5.56463 (  189)
  link_BETA1-6         : bond        0.00165 (    1)
  link_BETA1-6         : angle       1.37854 (    3)
  SS BOND              : bond        0.00410 (    5)
  SS BOND              : angle       0.83457 (   10)
  covalent geometry    : bond        0.00383 ( 3472)
  covalent geometry    : angle       0.69427 ( 4720)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1630.33 seconds
wall clock time: 28 minutes 54.87 seconds (1734.87 seconds total)