Starting phenix.real_space_refine
on Fri Aug 22 14:42:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xb4_38210/08_2025/8xb4_38210.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xb4_38210/08_2025/8xb4_38210.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xb4_38210/08_2025/8xb4_38210.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xb4_38210/08_2025/8xb4_38210.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xb4_38210/08_2025/8xb4_38210.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xb4_38210/08_2025/8xb4_38210.map"
  }
  resolution = 2.92
  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=  -0.001 sd=   0.126
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      20      5.16       5
     C    2894      2.51       5
     N     665      2.21       5
     O     728      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4307
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 536, 4293
          Classifications: {'peptide': 536}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 516}
          Chain breaks: 2
    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: 1.33, per 1000 atoms: 0.31
  Number of scatterers: 4307
  At special positions: 0
  Unit cell: (65.88, 66.96, 95.04, 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      20     16.00
     O     728      8.00
     N     665      7.00
     C    2894      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 176 " - pdb=" SG  CYS A 185 " 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
    NAG-ASN
      " NAG A 701 " - " ASN A 184 "
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 168.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  988

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 0 sheets defined
      81.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 74
      removed outlier: 4.005A  pdb=" N   PHE A  72 " --> pdb=" O   SER A  68 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   VAL A  74 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 90
      removed outlier: 3.525A  pdb=" N   VAL A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   PHE A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      Proline residue:  A  83  - end of helix
    Processing helix  chain 'A' and resid 91 through 105
      removed outlier: 3.652A  pdb=" N   LEU A  95 " --> pdb=" O   GLY A  91 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
    Processing helix  chain 'A' and resid 105 through 121
      removed outlier: 3.524A  pdb=" N   LEU A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.870A  pdb=" N   TRP A 128 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE A 130 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 166
      removed outlier: 3.805A  pdb=" N   GLY A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 207
      removed outlier: 3.505A  pdb=" N   PHE A 207 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 204 through 207'
    Processing helix  chain 'A' and resid 208 through 218
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 264 through 283
      Proline residue:  A 270  - end of helix
    Processing helix  chain 'A' and resid 286 through 296
      removed outlier: 3.865A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.788A  pdb=" N   LEU A 302 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 320
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 338 through 372
    Processing helix  chain 'A' and resid 375 through 379
      removed outlier: 3.542A  pdb=" N   VAL A 379 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 396
      Proline residue:  A 392  - end of helix
    Processing helix  chain 'A' and resid 400 through 435
    Processing helix  chain 'A' and resid 435 through 441
    Processing helix  chain 'A' and resid 441 through 456
    Processing helix  chain 'A' and resid 464 through 476
      removed outlier: 3.731A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 494
    Processing helix  chain 'A' and resid 497 through 509
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 4.293A  pdb=" N   SER A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 578
    Processing helix  chain 'A' and resid 583 through 593
    Processing helix  chain 'A' and resid 594 through 597
    Processing helix  chain 'A' and resid 598 through 603
      removed outlier: 4.038A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 598 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLN A 603 " --> pdb=" O   HIS A 599 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 598 through 603'
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 4.316A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)

    278 hydrogen bonds defined for protein.
    819 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: 0.67

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1257
        1.34 -     1.46: 1195
        1.46 -     1.58: 1964
        1.58 -     1.70: 0
        1.70 -     1.81: 31
  Bond restraints: 4447
  Sorted by residual:
  bond pdb=" C3  NAG A 701 "
       pdb=" O3  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.86e-01
  bond pdb=" C5  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.413  1.432 -0.019 2.00e-02 2.50e+03 9.34e-01
  bond pdb=" CG  LEU A 390 "
       pdb=" CD2 LEU A 390 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.20e-01
  bond pdb=" C   PHE A  82 "
       pdb=" O   PHE A  82 "
    ideal  model  delta    sigma   weight residual
    1.244  1.235  0.008 9.80e-03 1.04e+04 6.95e-01
  bond pdb=" CB  VAL A 535 "
       pdb=" CG1 VAL A 535 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 3.30e-02 9.18e+02 6.43e-01
  ... (remaining 4442 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 5756
        1.18 -     2.36: 249
        2.36 -     3.54: 45
        3.54 -     4.72: 11
        4.72 -     5.90: 8
  Bond angle restraints: 6069
  Sorted by residual:
  angle pdb=" N   GLY A 478 "
        pdb=" CA  GLY A 478 "
        pdb=" C   GLY A 478 "
      ideal   model   delta    sigma   weight residual
     113.18  107.55    5.63 2.37e+00 1.78e-01 5.64e+00
  angle pdb=" C   ASN A 596 "
        pdb=" N   GLU A 597 "
        pdb=" CA  GLU A 597 "
      ideal   model   delta    sigma   weight residual
     123.17  120.08    3.09 1.49e+00 4.50e-01 4.30e+00
  angle pdb=" CA  TYR A 391 "
        pdb=" C   TYR A 391 "
        pdb=" N   PRO A 392 "
      ideal   model   delta    sigma   weight residual
     118.44  121.69   -3.25 1.59e+00 3.96e-01 4.17e+00
  angle pdb=" C   VAL A 282 "
        pdb=" N   THR A 283 "
        pdb=" CA  THR A 283 "
      ideal   model   delta    sigma   weight residual
     121.94  118.02    3.92 2.00e+00 2.50e-01 3.85e+00
  angle pdb=" CA  TYR A 111 "
        pdb=" CB  TYR A 111 "
        pdb=" CG  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     113.90  117.28   -3.38 1.80e+00 3.09e-01 3.53e+00
  ... (remaining 6064 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.48: 2352
       21.48 -    42.95: 121
       42.95 -    64.43: 8
       64.43 -    85.90: 7
       85.90 -   107.38: 7
  Dihedral angle restraints: 2495
    sinusoidal: 944
      harmonic: 1551
  Sorted by residual:
  dihedral pdb=" CA  THR A 544 "
           pdb=" C   THR A 544 "
           pdb=" N   TYR A 545 "
           pdb=" CA  TYR A 545 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.23   19.77     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" C2  NAG A 701 "
           pdb=" C3  NAG A 701 "
           pdb=" C4  NAG A 701 "
           pdb=" C5  NAG A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.78  -53.60  107.38     1      3.00e+01 1.11e-03 1.39e+01
  dihedral pdb=" C2  NAG A 701 "
           pdb=" C3  NAG A 701 "
           pdb=" C4  NAG A 701 "
           pdb=" O4  NAG A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   68.05  107.06     1      3.00e+01 1.11e-03 1.38e+01
  ... (remaining 2492 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 360
       0.029 -    0.058: 208
       0.058 -    0.087: 78
       0.087 -    0.116: 27
       0.116 -    0.145: 8
  Chirality restraints: 681
  Sorted by residual:
  chirality pdb=" C1  NAG A 701 "
            pdb=" ND2 ASN A 184 "
            pdb=" C2  NAG A 701 "
            pdb=" O5  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 5.25e-01
  chirality pdb=" CA  PRO A 132 "
            pdb=" N   PRO A 132 "
            pdb=" C   PRO A 132 "
            pdb=" CB  PRO A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.98e-01
  chirality pdb=" CA  ILE A 549 "
            pdb=" N   ILE A 549 "
            pdb=" C   ILE A 549 "
            pdb=" CB  ILE A 549 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 678 not shown)

  Planarity restraints: 737
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  82 "   -0.030 5.00e-02 4.00e+02   4.47e-02 3.20e+00
        pdb=" N   PRO A  83 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A  83 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  83 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 111 "   -0.014 2.00e-02 2.50e+03   1.23e-02 3.01e+00
        pdb=" CG  TYR A 111 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 111 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 111 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 391 "   -0.029 5.00e-02 4.00e+02   4.31e-02 2.98e+00
        pdb=" N   PRO A 392 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 392 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 392 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 734 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1130
        2.79 -     3.32: 4134
        3.32 -     3.84: 7479
        3.84 -     4.37: 9160
        4.37 -     4.90: 15607
  Nonbonded interactions: 37510
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 496 "
            pdb=" OD2 ASP A 504 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OE2 GLU A 425 "
            pdb=" OG1 THR A 429 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" NH1 ARG A 121 "
            pdb=" O   ASN A 333 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" OD1 ASP A  75 "
            pdb=" OD1 ASN A  78 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   ALA A 589 "
            pdb=" OG1 THR A 593 "
     model   vdw
     2.369 3.040
  ... (remaining 37505 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             1.660
  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:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.390
  Find NCS groups from input model:        0.020
  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:8.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
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      :  0.005   0.038   4449  Z= 0.193
  Angle     :  0.606   5.903   6074  Z= 0.329
  Chirality :  0.043   0.145    681
  Planarity :  0.005   0.045    736
  Dihedral  : 14.468 107.378   1504
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.88 (0.32), residues: 530
  helix: -1.09 (0.23), residues: 379
  sheet:  None (None), residues: 0
  loop : -1.19 (0.47), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 341 
 TYR   0.030   0.002   TYR A 111 
 PHE   0.012   0.001   PHE A 316 
 TRP   0.027   0.001   TRP A 253 
 HIS   0.005   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 4447)
  covalent geometry    : angle       0.60558 ( 6069)
  SS BOND              : bond        0.00067 (    1)
  SS BOND              : angle       1.17762 (    2)
  hydrogen bonds       : bond        0.15009 (  278)
  hydrogen bonds       : angle       6.81434 (  819)
  link_NAG-ASN         : bond        0.00459 (    1)
  link_NAG-ASN         : angle       0.93323 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A   88 LYS cc_start: 0.8339 (tttp) cc_final: 0.8020 (ttmt)
REVERT: A  206 LYS cc_start: 0.7992 (pttm) cc_final: 0.7682 (ptpt)
REVERT: A  531 PHE cc_start: 0.7634 (t80) cc_final: 0.7178 (t80)
  outliers start: 0
  outliers final: 1
  residues processed: 75
  average time/residue: 0.3617
  time to fit residues: 28.8097
Evaluate side-chains
  54 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0270
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
A 222 HIS
A 603 GLN
A 610 GLN
A 613 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.135340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.114849 restraints weight = 5001.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.51
r_work: 0.3099 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4449  Z= 0.130
  Angle     :  0.551   6.848   6074  Z= 0.280
  Chirality :  0.042   0.188    681
  Planarity :  0.005   0.044    736
  Dihedral  :  5.678  28.833    600
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  8.63 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.35), residues: 530
  helix:  0.14 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.36 (0.53), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 604 
 TYR   0.018   0.001   TYR A 111 
 PHE   0.012   0.001   PHE A 110 
 TRP   0.010   0.001   TRP A 553 
 HIS   0.003   0.001   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4447)
  covalent geometry    : angle       0.55042 ( 6069)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       1.08104 (    2)
  hydrogen bonds       : bond        0.04186 (  278)
  hydrogen bonds       : angle       4.74898 (  819)
  link_NAG-ASN         : bond        0.00649 (    1)
  link_NAG-ASN         : angle       1.39768 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.8199 (pttm) cc_final: 0.7639 (ptpt)
REVERT: A  586 GLU cc_start: 0.6268 (pt0) cc_final: 0.6043 (tm-30)
REVERT: A  615 LEU cc_start: 0.8213 (mp) cc_final: 0.7990 (mp)
  outliers start: 8
  outliers final: 1
  residues processed: 69
  average time/residue: 0.3775
  time to fit residues: 27.6072
Evaluate side-chains
  53 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0670
   chunk 26 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 603 GLN
A 610 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.133957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.113278 restraints weight = 4990.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.51
r_work: 0.3157 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4449  Z= 0.137
  Angle     :  0.526   5.942   6074  Z= 0.270
  Chirality :  0.041   0.145    681
  Planarity :  0.005   0.045    736
  Dihedral  :  4.655  30.853    600
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.28 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.36), residues: 530
  helix:  0.62 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.27 (0.53), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 341 
 TYR   0.018   0.001   TYR A 111 
 PHE   0.011   0.001   PHE A 408 
 TRP   0.010   0.001   TRP A 553 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4447)
  covalent geometry    : angle       0.52468 ( 6069)
  SS BOND              : bond        0.00241 (    1)
  SS BOND              : angle       1.29685 (    2)
  hydrogen bonds       : bond        0.04208 (  278)
  hydrogen bonds       : angle       4.56484 (  819)
  link_NAG-ASN         : bond        0.00427 (    1)
  link_NAG-ASN         : angle       1.34716 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.8275 (pttm) cc_final: 0.7746 (ptpt)
REVERT: A  586 GLU cc_start: 0.6361 (pt0) cc_final: 0.6136 (tm-30)
REVERT: A  597 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7462 (pm20)
REVERT: A  615 LEU cc_start: 0.8289 (mp) cc_final: 0.8050 (mp)
  outliers start: 10
  outliers final: 2
  residues processed: 65
  average time/residue: 0.3632
  time to fit residues: 24.9929
Evaluate side-chains
  55 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  597 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 13 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.132582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.111955 restraints weight = 4967.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 1.48
r_work: 0.3113 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4449  Z= 0.149
  Angle     :  0.532   6.096   6074  Z= 0.275
  Chirality :  0.041   0.148    681
  Planarity :  0.004   0.046    736
  Dihedral  :  4.355  22.630    598
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 12.61 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.36), residues: 530
  helix:  0.81 (0.26), residues: 385
  sheet:  None (None), residues: 0
  loop : -0.19 (0.52), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 341 
 TYR   0.016   0.001   TYR A  84 
 PHE   0.011   0.001   PHE A 409 
 TRP   0.010   0.001   TRP A 553 
 HIS   0.003   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4447)
  covalent geometry    : angle       0.53175 ( 6069)
  SS BOND              : bond        0.00229 (    1)
  SS BOND              : angle       1.22717 (    2)
  hydrogen bonds       : bond        0.04263 (  278)
  hydrogen bonds       : angle       4.53375 (  819)
  link_NAG-ASN         : bond        0.00481 (    1)
  link_NAG-ASN         : angle       1.00628 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.8294 (pttm) cc_final: 0.7735 (ptpt)
REVERT: A  373 LYS cc_start: 0.7912 (mmtp) cc_final: 0.7502 (mmmt)
REVERT: A  615 LEU cc_start: 0.8183 (mp) cc_final: 0.7935 (mp)
  outliers start: 12
  outliers final: 4
  residues processed: 63
  average time/residue: 0.3292
  time to fit residues: 22.1628
Evaluate side-chains
  57 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  235 TRP
Chi-restraints excluded: chain A residue  418 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.132808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.112105 restraints weight = 5007.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.50
r_work: 0.3131 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4449  Z= 0.151
  Angle     :  0.531   6.128   6074  Z= 0.273
  Chirality :  0.041   0.142    681
  Planarity :  0.004   0.046    736
  Dihedral  :  4.349  21.826    598
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.50 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.36), residues: 530
  helix:  0.88 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.04 (0.53), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 604 
 TYR   0.017   0.001   TYR A  84 
 PHE   0.013   0.001   PHE A 408 
 TRP   0.010   0.001   TRP A 553 
 HIS   0.003   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4447)
  covalent geometry    : angle       0.53030 ( 6069)
  SS BOND              : bond        0.00233 (    1)
  SS BOND              : angle       1.25181 (    2)
  hydrogen bonds       : bond        0.04251 (  278)
  hydrogen bonds       : angle       4.49177 (  819)
  link_NAG-ASN         : bond        0.00469 (    1)
  link_NAG-ASN         : angle       0.87030 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.8386 (pttm) cc_final: 0.7801 (ptpt)
REVERT: A  586 GLU cc_start: 0.6420 (pt0) cc_final: 0.6171 (tm-30)
REVERT: A  597 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7224 (pm20)
REVERT: A  615 LEU cc_start: 0.8201 (mp) cc_final: 0.7966 (mp)
  outliers start: 12
  outliers final: 6
  residues processed: 64
  average time/residue: 0.3840
  time to fit residues: 26.0660
Evaluate side-chains
  62 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  235 TRP
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  597 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 51 optimal weight:    0.0170
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.134424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.113843 restraints weight = 5053.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.51
r_work: 0.3142 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4449  Z= 0.124
  Angle     :  0.507   6.042   6074  Z= 0.261
  Chirality :  0.040   0.139    681
  Planarity :  0.004   0.045    736
  Dihedral  :  4.178  18.783    598
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.94 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.37), residues: 530
  helix:  1.04 (0.26), residues: 387
  sheet:  None (None), residues: 0
  loop :  0.09 (0.54), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 604 
 TYR   0.015   0.001   TYR A  84 
 PHE   0.011   0.001   PHE A 110 
 TRP   0.010   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4447)
  covalent geometry    : angle       0.50663 ( 6069)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       1.02916 (    2)
  hydrogen bonds       : bond        0.03919 (  278)
  hydrogen bonds       : angle       4.34946 (  819)
  link_NAG-ASN         : bond        0.00468 (    1)
  link_NAG-ASN         : angle       0.87686 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  373 LYS cc_start: 0.7866 (mmtp) cc_final: 0.7650 (mmmt)
REVERT: A  586 GLU cc_start: 0.6312 (pt0) cc_final: 0.6074 (tm-30)
REVERT: A  597 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7156 (pm20)
REVERT: A  615 LEU cc_start: 0.8171 (mp) cc_final: 0.7923 (mp)
  outliers start: 13
  outliers final: 6
  residues processed: 68
  average time/residue: 0.3468
  time to fit residues: 25.0708
Evaluate side-chains
  62 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  235 TRP
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  597 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.132058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.111857 restraints weight = 5032.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.43
r_work: 0.3099 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4449  Z= 0.179
  Angle     :  0.559   6.281   6074  Z= 0.288
  Chirality :  0.042   0.143    681
  Planarity :  0.005   0.046    736
  Dihedral  :  4.423  21.258    598
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.27 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.36), residues: 530
  helix:  0.88 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop :  0.00 (0.54), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 604 
 TYR   0.019   0.002   TYR A  84 
 PHE   0.015   0.001   PHE A 316 
 TRP   0.010   0.001   TRP A 553 
 HIS   0.003   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 4447)
  covalent geometry    : angle       0.55853 ( 6069)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       1.39406 (    2)
  hydrogen bonds       : bond        0.04474 (  278)
  hydrogen bonds       : angle       4.55415 (  819)
  link_NAG-ASN         : bond        0.00440 (    1)
  link_NAG-ASN         : angle       0.76901 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  373 LYS cc_start: 0.7798 (mmtp) cc_final: 0.7519 (mmmt)
REVERT: A  597 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7225 (pm20)
  outliers start: 11
  outliers final: 6
  residues processed: 61
  average time/residue: 0.3368
  time to fit residues: 21.9433
Evaluate side-chains
  61 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  235 TRP
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  597 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0050
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5394

-------------------------------------------------------------------------------
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 = 0.3435 r_free = 0.3435 target = 0.133475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.113063 restraints weight = 4969.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 1.48
r_work: 0.3114 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4449  Z= 0.132
  Angle     :  0.520   6.200   6074  Z= 0.268
  Chirality :  0.040   0.138    681
  Planarity :  0.004   0.046    736
  Dihedral  :  4.254  18.956    598
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.93 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.37), residues: 530
  helix:  1.03 (0.26), residues: 387
  sheet:  None (None), residues: 0
  loop :  0.12 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 604 
 TYR   0.015   0.001   TYR A  84 
 PHE   0.011   0.001   PHE A 409 
 TRP   0.010   0.001   TRP A 553 
 HIS   0.003   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4447)
  covalent geometry    : angle       0.51921 ( 6069)
  SS BOND              : bond        0.00210 (    1)
  SS BOND              : angle       1.12512 (    2)
  hydrogen bonds       : bond        0.04006 (  278)
  hydrogen bonds       : angle       4.40529 (  819)
  link_NAG-ASN         : bond        0.00468 (    1)
  link_NAG-ASN         : angle       0.80417 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  596 ASN cc_start: 0.7049 (p0) cc_final: 0.6705 (p0)
  outliers start: 10
  outliers final: 6
  residues processed: 62
  average time/residue: 0.3360
  time to fit residues: 22.2729
Evaluate side-chains
  62 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  235 TRP
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  418 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3417 r_free = 0.3417 target = 0.132129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.111530 restraints weight = 5017.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.49
r_work: 0.3118 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4449  Z= 0.152
  Angle     :  0.544   6.210   6074  Z= 0.280
  Chirality :  0.041   0.156    681
  Planarity :  0.004   0.046    736
  Dihedral  :  4.313  19.375    598
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.37 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.37), residues: 530
  helix:  1.03 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop :  0.07 (0.54), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 604 
 TYR   0.017   0.001   TYR A  84 
 PHE   0.013   0.001   PHE A 316 
 TRP   0.010   0.001   TRP A 553 
 HIS   0.003   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4447)
  covalent geometry    : angle       0.54331 ( 6069)
  SS BOND              : bond        0.00231 (    1)
  SS BOND              : angle       1.25737 (    2)
  hydrogen bonds       : bond        0.04221 (  278)
  hydrogen bonds       : angle       4.46602 (  819)
  link_NAG-ASN         : bond        0.00464 (    1)
  link_NAG-ASN         : angle       0.77738 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  596 ASN cc_start: 0.6947 (p0) cc_final: 0.6619 (p0)
  outliers start: 9
  outliers final: 6
  residues processed: 57
  average time/residue: 0.3367
  time to fit residues: 20.5256
Evaluate side-chains
  58 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  235 TRP
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  418 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3421 r_free = 0.3421 target = 0.132276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.111677 restraints weight = 5009.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.48
r_work: 0.3099 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4449  Z= 0.157
  Angle     :  0.554   6.291   6074  Z= 0.285
  Chirality :  0.041   0.154    681
  Planarity :  0.004   0.046    736
  Dihedral  :  4.364  19.721    598
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.04 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.37), residues: 530
  helix:  0.99 (0.26), residues: 388
  sheet:  None (None), residues: 0
  loop :  0.08 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 604 
 TYR   0.017   0.001   TYR A  84 
 PHE   0.013   0.001   PHE A 316 
 TRP   0.010   0.001   TRP A 553 
 HIS   0.003   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4447)
  covalent geometry    : angle       0.55377 ( 6069)
  SS BOND              : bond        0.00214 (    1)
  SS BOND              : angle       1.30153 (    2)
  hydrogen bonds       : bond        0.04274 (  278)
  hydrogen bonds       : angle       4.49768 (  819)
  link_NAG-ASN         : bond        0.00451 (    1)
  link_NAG-ASN         : angle       0.76702 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  596 ASN cc_start: 0.6908 (p0) cc_final: 0.6578 (p0)
  outliers start: 7
  outliers final: 6
  residues processed: 55
  average time/residue: 0.3210
  time to fit residues: 19.0346
Evaluate side-chains
  59 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  235 TRP
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  418 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 45 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0970
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.3460 r_free = 0.3460 target = 0.135268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.115552 restraints weight = 4965.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.41
r_work: 0.3138 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4449  Z= 0.121
  Angle     :  0.520   6.044   6074  Z= 0.267
  Chirality :  0.040   0.148    681
  Planarity :  0.004   0.046    736
  Dihedral  :  4.141  16.931    598
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.48 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.37), residues: 530
  helix:  1.17 (0.26), residues: 388
  sheet:  None (None), residues: 0
  loop :  0.25 (0.56), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 604 
 TYR   0.015   0.001   TYR A  84 
 PHE   0.011   0.001   PHE A 110 
 TRP   0.010   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4447)
  covalent geometry    : angle       0.51907 ( 6069)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       1.07813 (    2)
  hydrogen bonds       : bond        0.03832 (  278)
  hydrogen bonds       : angle       4.33376 (  819)
  link_NAG-ASN         : bond        0.00469 (    1)
  link_NAG-ASN         : angle       0.84328 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1541.02 seconds
wall clock time: 27 minutes 16.14 seconds (1636.14 seconds total)