Starting phenix.real_space_refine
on Tue Mar  3 10:49:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jzm_22533/03_2026/7jzm_22533.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jzm_22533/03_2026/7jzm_22533.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jzm_22533/03_2026/7jzm_22533.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jzm_22533/03_2026/7jzm_22533.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jzm_22533/03_2026/7jzm_22533.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jzm_22533/03_2026/7jzm_22533.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.022
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      10      5.16       5
     C    1310      2.51       5
     N     340      2.21       5
     O     373      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2033
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 495
          Classifications: {'peptide': 64}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'TRANS': 63}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 7}
          Unresolved non-hydrogen planarities: 40
    Chain: "B"
      Number of atoms: 1500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1500
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.02, per 1000 atoms: 0.50
  Number of scatterers: 2033
  At special positions: 0
  Unit cell: (66.15, 68.25, 69.3, 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      10     16.00
     O     373      8.00
     N     340      7.00
     C    1310      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.28
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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 C   1 " - " NAG C   2 "
    BETA1-6
      " NAG C   1 " - " FUC C   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG C   1 " - " ASN B 343 "
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 81.3 milliseconds
  

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  486

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 4 sheets defined
      38.4% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 17
    Processing helix  chain 'A' and resid 22 through 42
    Processing helix  chain 'A' and resid 44 through 64
    Processing helix  chain 'B' and resid 337 through 341
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.804A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 389
      removed outlier: 3.514A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.158A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.670A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.479A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474

    93 hydrogen bonds defined for protein.
    240 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: 0.29

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 591
        1.33 -     1.46: 586
        1.46 -     1.59: 893
        1.59 -     1.72: 0
        1.72 -     1.85: 12
  Bond restraints: 2082
  Sorted by residual:
  bond pdb=" N   PRO B 499 "
       pdb=" CD  PRO B 499 "
    ideal  model  delta    sigma   weight residual
    1.473  1.337  0.136 1.40e-02 5.10e+03 9.45e+01
  bond pdb=" C5  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.479 -0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" CG  GLN B 506 "
       pdb=" CD  GLN B 506 "
    ideal  model  delta    sigma   weight residual
    1.516  1.438  0.078 2.50e-02 1.60e+03 9.74e+00
  bond pdb=" C5  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.38e+00
  bond pdb=" C5  FUC C   3 "
       pdb=" O5  FUC C   3 "
    ideal  model  delta    sigma   weight residual
    1.423  1.477 -0.054 2.00e-02 2.50e+03 7.29e+00
  ... (remaining 2077 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 2649
        2.56 -     5.12: 157
        5.12 -     7.69: 20
        7.69 -    10.25: 3
       10.25 -    12.81: 1
  Bond angle restraints: 2830
  Sorted by residual:
  angle pdb=" N   PRO B 499 "
        pdb=" CA  PRO B 499 "
        pdb=" CB  PRO B 499 "
      ideal   model   delta    sigma   weight residual
     103.41   96.76    6.65 9.40e-01 1.13e+00 5.01e+01
  angle pdb=" CA  PRO B 499 "
        pdb=" N   PRO B 499 "
        pdb=" CD  PRO B 499 "
      ideal   model   delta    sigma   weight residual
     112.00  120.93   -8.93 1.40e+00 5.10e-01 4.07e+01
  angle pdb=" C   ALA B 520 "
        pdb=" N   PRO B 521 "
        pdb=" CA  PRO B 521 "
      ideal   model   delta    sigma   weight residual
     119.56  126.01   -6.45 1.02e+00 9.61e-01 4.00e+01
  angle pdb=" C   GLN B 498 "
        pdb=" N   PRO B 499 "
        pdb=" CA  PRO B 499 "
      ideal   model   delta    sigma   weight residual
     119.87  126.31   -6.44 1.04e+00 9.25e-01 3.84e+01
  angle pdb=" C   PHE B 490 "
        pdb=" N   PRO B 491 "
        pdb=" CA  PRO B 491 "
      ideal   model   delta    sigma   weight residual
     119.56  125.65   -6.09 1.01e+00 9.80e-01 3.64e+01
  ... (remaining 2825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.30: 1208
       14.30 -    28.59: 48
       28.59 -    42.89: 8
       42.89 -    57.18: 5
       57.18 -    71.48: 3
  Dihedral angle restraints: 1272
    sinusoidal: 513
      harmonic: 759
  Sorted by residual:
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.36   41.64     1      1.00e+01 1.00e-02 2.43e+01
  dihedral pdb=" CB  GLU B 484 "
           pdb=" CG  GLU B 484 "
           pdb=" CD  GLU B 484 "
           pdb=" OE1 GLU B 484 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   71.48  -71.48     1      3.00e+01 1.11e-03 7.28e+00
  dihedral pdb=" CA  ALA B 520 "
           pdb=" C   ALA B 520 "
           pdb=" N   PRO B 521 "
           pdb=" CA  PRO B 521 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.92   13.08     0      5.00e+00 4.00e-02 6.85e+00
  ... (remaining 1269 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 230
       0.082 -    0.164: 69
       0.164 -    0.245: 15
       0.245 -    0.327: 3
       0.327 -    0.409: 1
  Chirality restraints: 318
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.59    0.19 2.00e-02 2.50e+03 9.38e+01
  chirality pdb=" C1  FUC C   3 "
            pdb=" O6  NAG C   1 "
            pdb=" C2  FUC C   3 "
            pdb=" O5  FUC C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.48    0.08 2.00e-02 2.50e+03 1.68e+01
  chirality pdb=" C2  NAG C   2 "
            pdb=" C1  NAG C   2 "
            pdb=" C3  NAG C   2 "
            pdb=" N2  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.90    0.41 2.00e-01 2.50e+01 4.18e+00
  ... (remaining 315 not shown)

  Planarity restraints: 364
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 495 "    0.036 2.00e-02 2.50e+03   1.86e-02 6.92e+00
        pdb=" CG  TYR B 495 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 495 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 495 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 495 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 495 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 495 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 495 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 453 "    0.025 2.00e-02 2.50e+03   1.34e-02 3.57e+00
        pdb=" CG  TYR B 453 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 453 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 453 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 453 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 453 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 453 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B 453 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 343 "   -0.016 2.00e-02 2.50e+03   1.65e-02 3.40e+00
        pdb=" CG  ASN B 343 "    0.007 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 343 "    0.004 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 343 "    0.025 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 361 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 880
        2.92 -     3.41: 1816
        3.41 -     3.91: 3445
        3.91 -     4.40: 3881
        4.40 -     4.90: 6261
  Nonbonded interactions: 16283
  Sorted by model distance:
  nonbonded pdb=" O   ASP A   2 "
            pdb=" OD1 ASP A   2 "
     model   vdw
     2.420 3.040
  nonbonded pdb=" N   ASP B 428 "
            pdb=" OD1 ASP B 428 "
     model   vdw
     2.566 3.120
  nonbonded pdb=" O   ASN B 501 "
            pdb=" NE2 GLN B 506 "
     model   vdw
     2.568 3.120
  nonbonded pdb=" O5  NAG C   1 "
            pdb=" O6  NAG C   1 "
     model   vdw
     2.569 2.432
  nonbonded pdb=" N   SER B 373 "
            pdb=" N   PHE B 374 "
     model   vdw
     2.574 2.560
  ... (remaining 16278 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.140
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.020
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
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      :  0.016   0.245   2089  Z= 0.861
  Angle     :  1.414  12.996   2847  Z= 0.931
  Chirality :  0.084   0.409    318
  Planarity :  0.005   0.026    363
  Dihedral  :  9.533  71.478    774
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 1.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  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 are not related in a simple way.
  whole:  0.75 (0.52), residues: 254
  helix:  0.21 (0.51), residues: 85
  sheet:  0.78 (0.76), residues: 52
  loop :  0.82 (0.60), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 355 
 TYR   0.036   0.006   TYR B 495 
 PHE   0.013   0.002   PHE B 342 
 TRP   0.012   0.005   TRP B 353 
 HIS   0.002   0.001   HIS A   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.01477 ( 2082)
  covalent geometry    : angle       1.37761 ( 2830)
  SS BOND              : bond        0.12244 (    4)
  SS BOND              : angle       5.43319 (    8)
  hydrogen bonds       : bond        0.15984 (   93)
  hydrogen bonds       : angle       7.20776 (  240)
  link_BETA1-4         : bond        0.07488 (    1)
  link_BETA1-4         : angle       3.76318 (    3)
  link_BETA1-6         : bond        0.05859 (    1)
  link_BETA1-6         : angle       2.72093 (    3)
  link_NAG-ASN         : bond        0.05758 (    1)
  link_NAG-ASN         : angle       2.63632 (    3)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.076 
Fit side-chains
REVERT: B  469 SER cc_start: 0.8425 (t) cc_final: 0.7858 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0856
  time to fit residues: 6.3348
Evaluate side-chains
  42 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    0.3980
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0870
   chunk 16 optimal weight:    0.2980
   chunk 15 optimal weight:    0.3980
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    0.1980
   chunk 6 optimal weight:    0.0050
   overall best weight:    0.1972

-------------------------------------------------------------------------------
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 = 0.3581 r_free = 0.3581 target = 0.131654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.116200 restraints weight = 2960.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.119167 restraints weight = 1602.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.121154 restraints weight = 1072.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.122316 restraints weight = 815.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.123274 restraints weight = 679.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2089  Z= 0.160
  Angle     :  0.654   8.040   2847  Z= 0.343
  Chirality :  0.044   0.144    318
  Planarity :  0.004   0.039    363
  Dihedral  :  6.134  58.005    344
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  :  9.95 %
    Favored  : 87.56 %
  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 are not related in a simple way.
  whole:  1.01 (0.54), residues: 254
  helix:  1.04 (0.58), residues: 88
  sheet:  0.60 (0.79), residues: 49
  loop :  0.60 (0.57), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 454 
 TYR   0.019   0.002   TYR B 495 
 PHE   0.016   0.002   PHE A  33 
 TRP   0.009   0.002   TRP B 436 
 HIS   0.001   0.000   HIS A   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 2082)
  covalent geometry    : angle       0.64628 ( 2830)
  SS BOND              : bond        0.00797 (    4)
  SS BOND              : angle       1.54027 (    8)
  hydrogen bonds       : bond        0.05653 (   93)
  hydrogen bonds       : angle       5.36331 (  240)
  link_BETA1-4         : bond        0.00238 (    1)
  link_BETA1-4         : angle       1.38533 (    3)
  link_BETA1-6         : bond        0.01014 (    1)
  link_BETA1-6         : angle       1.45526 (    3)
  link_NAG-ASN         : bond        0.00070 (    1)
  link_NAG-ASN         : angle       1.22392 (    3)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 ILE cc_start: 0.8245 (mm) cc_final: 0.7818 (mt)
  outliers start: 5
  outliers final: 3
  residues processed: 41
  average time/residue: 0.0578
  time to fit residues: 2.8373
Evaluate side-chains
  39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 10 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 12 optimal weight:    0.3980
   chunk 23 optimal weight:    0.3980
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    0.2980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
A   6 HIS
A  43 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.125047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.108996 restraints weight = 3086.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.111843 restraints weight = 1695.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.113830 restraints weight = 1144.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.114947 restraints weight = 870.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.115835 restraints weight = 732.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2089  Z= 0.227
  Angle     :  0.617   5.871   2847  Z= 0.331
  Chirality :  0.044   0.145    318
  Planarity :  0.004   0.040    363
  Dihedral  :  6.424  59.487    344
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  :  8.96 %
    Favored  : 88.56 %
  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 are not related in a simple way.
  whole:  0.51 (0.52), residues: 254
  helix:  0.89 (0.56), residues: 89
  sheet: -0.06 (0.74), residues: 49
  loop :  0.26 (0.57), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 509 
 TYR   0.019   0.002   TYR B 453 
 PHE   0.015   0.002   PHE B 429 
 TRP   0.013   0.002   TRP B 436 
 HIS   0.003   0.002   HIS A   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 2082)
  covalent geometry    : angle       0.60709 ( 2830)
  SS BOND              : bond        0.01057 (    4)
  SS BOND              : angle       1.59109 (    8)
  hydrogen bonds       : bond        0.04717 (   93)
  hydrogen bonds       : angle       5.25247 (  240)
  link_BETA1-4         : bond        0.00367 (    1)
  link_BETA1-4         : angle       1.06310 (    3)
  link_BETA1-6         : bond        0.00768 (    1)
  link_BETA1-6         : angle       1.94921 (    3)
  link_NAG-ASN         : bond        0.00097 (    1)
  link_NAG-ASN         : angle       1.44568 (    3)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 ILE cc_start: 0.8461 (mm) cc_final: 0.8077 (mt)
REVERT: A   34 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7708 (mp0)
  outliers start: 5
  outliers final: 3
  residues processed: 44
  average time/residue: 0.0720
  time to fit residues: 3.6482
Evaluate side-chains
  40 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 4 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 24 optimal weight:    0.2980
   chunk 18 optimal weight:    0.2980
   chunk 23 optimal weight:    0.1980
   chunk 19 optimal weight:    0.1980
   chunk 9 optimal weight:    0.0060
   overall best weight:    0.1596

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

Flipped N/Q/H residues before XYZ refinement:
A  18 HIS
B 498 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.127499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.111344 restraints weight = 3009.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.114151 restraints weight = 1694.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.116043 restraints weight = 1159.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.117307 restraints weight = 893.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.117917 restraints weight = 741.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2089  Z= 0.122
  Angle     :  0.540   5.129   2847  Z= 0.281
  Chirality :  0.041   0.133    318
  Planarity :  0.004   0.041    363
  Dihedral  :  6.051  58.885    344
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  :  9.45 %
    Favored  : 87.06 %
  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 are not related in a simple way.
  whole:  0.54 (0.52), residues: 254
  helix:  1.01 (0.57), residues: 88
  sheet: -0.22 (0.73), residues: 49
  loop :  0.28 (0.57), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 457 
 TYR   0.010   0.001   TYR B 495 
 PHE   0.013   0.001   PHE A  33 
 TRP   0.011   0.002   TRP B 436 
 HIS   0.002   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 2082)
  covalent geometry    : angle       0.53163 ( 2830)
  SS BOND              : bond        0.00435 (    4)
  SS BOND              : angle       1.33605 (    8)
  hydrogen bonds       : bond        0.04040 (   93)
  hydrogen bonds       : angle       4.94948 (  240)
  link_BETA1-4         : bond        0.00376 (    1)
  link_BETA1-4         : angle       1.13476 (    3)
  link_BETA1-6         : bond        0.00755 (    1)
  link_BETA1-6         : angle       1.41849 (    3)
  link_NAG-ASN         : bond        0.00013 (    1)
  link_NAG-ASN         : angle       1.27453 (    3)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.8453 (mm) cc_final: 0.8106 (mt)
REVERT: A   34 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7324 (mp0)
REVERT: B  489 TYR cc_start: 0.7650 (m-80) cc_final: 0.6594 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 44
  average time/residue: 0.0588
  time to fit residues: 3.0816
Evaluate side-chains
  38 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0670
   chunk 13 optimal weight:    0.1980
   chunk 18 optimal weight:    0.0970
   chunk 22 optimal weight:    0.5980
   chunk 3 optimal weight:    0.3980
   chunk 10 optimal weight:    0.1980
   chunk 23 optimal weight:    0.0980
   overall best weight:    0.1316

-------------------------------------------------------------------------------
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 = 0.3554 r_free = 0.3554 target = 0.128002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.111274 restraints weight = 3032.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.114219 restraints weight = 1678.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.116188 restraints weight = 1139.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.117349 restraints weight = 872.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.118331 restraints weight = 735.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2089  Z= 0.116
  Angle     :  0.565   9.222   2847  Z= 0.283
  Chirality :  0.041   0.131    318
  Planarity :  0.004   0.042    363
  Dihedral  :  5.918  58.589    344
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 13.93 %
    Favored  : 82.59 %
  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 are not related in a simple way.
  whole:  0.57 (0.53), residues: 254
  helix:  1.07 (0.58), residues: 88
  sheet: -0.21 (0.74), residues: 49
  loop :  0.28 (0.57), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 457 
 TYR   0.010   0.001   TYR B 495 
 PHE   0.012   0.001   PHE A  33 
 TRP   0.010   0.001   TRP B 436 
 HIS   0.001   0.001   HIS A   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 2082)
  covalent geometry    : angle       0.55940 ( 2830)
  SS BOND              : bond        0.00350 (    4)
  SS BOND              : angle       1.10471 (    8)
  hydrogen bonds       : bond        0.03687 (   93)
  hydrogen bonds       : angle       4.81805 (  240)
  link_BETA1-4         : bond        0.00364 (    1)
  link_BETA1-4         : angle       1.04229 (    3)
  link_BETA1-6         : bond        0.00863 (    1)
  link_BETA1-6         : angle       1.37171 (    3)
  link_NAG-ASN         : bond        0.00035 (    1)
  link_NAG-ASN         : angle       1.18846 (    3)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.8525 (mm) cc_final: 0.8163 (mt)
REVERT: A   34 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7252 (mp0)
REVERT: B  489 TYR cc_start: 0.7574 (m-80) cc_final: 0.6599 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 40
  average time/residue: 0.0585
  time to fit residues: 2.7895
Evaluate side-chains
  37 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0870
   chunk 9 optimal weight:    0.0570
   chunk 2 optimal weight:    0.0980
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 0 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0370
   chunk 4 optimal weight:    0.0970
   chunk 7 optimal weight:    0.0970
   overall best weight:    0.0750

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.129785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.112670 restraints weight = 2896.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.115632 restraints weight = 1625.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.117584 restraints weight = 1107.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.118862 restraints weight = 854.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.119621 restraints weight = 714.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2089  Z= 0.096
  Angle     :  0.490   4.990   2847  Z= 0.258
  Chirality :  0.041   0.129    318
  Planarity :  0.004   0.042    363
  Dihedral  :  5.780  58.333    344
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.43 %
    Favored  : 83.08 %
  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 are not related in a simple way.
  whole:  0.65 (0.54), residues: 254
  helix:  1.06 (0.58), residues: 88
  sheet: -0.11 (0.75), residues: 49
  loop :  0.36 (0.58), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 457 
 TYR   0.008   0.001   TYR A  14 
 PHE   0.010   0.001   PHE A  33 
 TRP   0.009   0.002   TRP B 436 
 HIS   0.000   0.000   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 2082)
  covalent geometry    : angle       0.48352 ( 2830)
  SS BOND              : bond        0.00354 (    4)
  SS BOND              : angle       1.14064 (    8)
  hydrogen bonds       : bond        0.03420 (   93)
  hydrogen bonds       : angle       4.64363 (  240)
  link_BETA1-4         : bond        0.00362 (    1)
  link_BETA1-4         : angle       1.03480 (    3)
  link_BETA1-6         : bond        0.00839 (    1)
  link_BETA1-6         : angle       1.27387 (    3)
  link_NAG-ASN         : bond        0.00076 (    1)
  link_NAG-ASN         : angle       1.06738 (    3)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A    9 MET cc_start: 0.7785 (tmm) cc_final: 0.7542 (ttp)
REVERT: A   25 ILE cc_start: 0.8549 (mm) cc_final: 0.8174 (mt)
REVERT: A   34 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7400 (mp0)
  outliers start: 5
  outliers final: 4
  residues processed: 34
  average time/residue: 0.0573
  time to fit residues: 2.3112
Evaluate side-chains
  35 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0370
   chunk 13 optimal weight:    0.0570
   chunk 15 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0570
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0970
   chunk 0 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0770
   chunk 18 optimal weight:    0.1980
   overall best weight:    0.0650

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.130113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.113003 restraints weight = 2987.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.115958 restraints weight = 1670.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.117845 restraints weight = 1136.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.119187 restraints weight = 879.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.119513 restraints weight = 733.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.4030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   2089  Z= 0.093
  Angle     :  0.491   5.430   2847  Z= 0.258
  Chirality :  0.040   0.128    318
  Planarity :  0.003   0.042    363
  Dihedral  :  5.761  57.979    344
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 13.43 %
    Favored  : 83.08 %
  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 are not related in a simple way.
  whole:  0.60 (0.54), residues: 254
  helix:  1.12 (0.58), residues: 88
  sheet: -0.01 (0.80), residues: 47
  loop :  0.17 (0.57), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 457 
 TYR   0.008   0.001   TYR A  14 
 PHE   0.010   0.001   PHE B 464 
 TRP   0.008   0.001   TRP B 436 
 HIS   0.000   0.000   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 2082)
  covalent geometry    : angle       0.48495 ( 2830)
  SS BOND              : bond        0.00304 (    4)
  SS BOND              : angle       1.10550 (    8)
  hydrogen bonds       : bond        0.03244 (   93)
  hydrogen bonds       : angle       4.56585 (  240)
  link_BETA1-4         : bond        0.00429 (    1)
  link_BETA1-4         : angle       1.01326 (    3)
  link_BETA1-6         : bond        0.00626 (    1)
  link_BETA1-6         : angle       1.20111 (    3)
  link_NAG-ASN         : bond        0.00093 (    1)
  link_NAG-ASN         : angle       1.03190 (    3)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.067 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.8572 (mm) cc_final: 0.8213 (mt)
REVERT: A   34 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7531 (mp0)
REVERT: A   59 LEU cc_start: 0.8827 (tp) cc_final: 0.8581 (tp)
  outliers start: 7
  outliers final: 5
  residues processed: 36
  average time/residue: 0.0515
  time to fit residues: 2.2624
Evaluate side-chains
  37 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0980
   chunk 5 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0670
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.3318

-------------------------------------------------------------------------------
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 = 0.3520 r_free = 0.3520 target = 0.125363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.108698 restraints weight = 3022.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.111521 restraints weight = 1696.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.113418 restraints weight = 1159.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.114560 restraints weight = 894.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.115441 restraints weight = 755.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   2089  Z= 0.197
  Angle     :  0.622  10.847   2847  Z= 0.316
  Chirality :  0.043   0.134    318
  Planarity :  0.004   0.043    363
  Dihedral  :  5.866  54.375    344
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 14.93 %
    Favored  : 81.59 %
  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 are not related in a simple way.
  whole:  0.38 (0.54), residues: 254
  helix:  1.05 (0.58), residues: 89
  sheet: -0.23 (0.81), residues: 49
  loop : -0.01 (0.57), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 457 
 TYR   0.015   0.002   TYR B 453 
 PHE   0.011   0.001   PHE B 490 
 TRP   0.008   0.002   TRP B 436 
 HIS   0.003   0.001   HIS A   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 2082)
  covalent geometry    : angle       0.61467 ( 2830)
  SS BOND              : bond        0.00251 (    4)
  SS BOND              : angle       1.24386 (    8)
  hydrogen bonds       : bond        0.03876 (   93)
  hydrogen bonds       : angle       4.89142 (  240)
  link_BETA1-4         : bond        0.00309 (    1)
  link_BETA1-4         : angle       1.01952 (    3)
  link_BETA1-6         : bond        0.00791 (    1)
  link_BETA1-6         : angle       1.69741 (    3)
  link_NAG-ASN         : bond        0.00200 (    1)
  link_NAG-ASN         : angle       1.49959 (    3)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 ILE cc_start: 0.8690 (mm) cc_final: 0.8304 (mt)
  outliers start: 7
  outliers final: 7
  residues processed: 38
  average time/residue: 0.0483
  time to fit residues: 2.2259
Evaluate side-chains
  43 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 8 optimal weight:    0.1980
   chunk 7 optimal weight:    0.3980
   chunk 1 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 14 optimal weight:    0.2980
   chunk 24 optimal weight:    0.3980
   chunk 17 optimal weight:    0.3980
   chunk 2 optimal weight:    0.0980
   chunk 11 optimal weight:    0.4980
   overall best weight:    0.2780

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.125672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.109072 restraints weight = 2981.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.111913 restraints weight = 1677.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.113823 restraints weight = 1146.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.115012 restraints weight = 883.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.115877 restraints weight = 744.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   2089  Z= 0.170
  Angle     :  0.604  10.275   2847  Z= 0.306
  Chirality :  0.043   0.130    318
  Planarity :  0.004   0.045    363
  Dihedral  :  5.777  52.768    344
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.42 %
    Favored  : 81.09 %
  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 are not related in a simple way.
  whole:  0.34 (0.54), residues: 254
  helix:  1.16 (0.58), residues: 89
  sheet: -0.45 (0.79), residues: 49
  loop : -0.07 (0.56), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 457 
 TYR   0.011   0.001   TYR B 453 
 PHE   0.010   0.001   PHE B 464 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.003   0.001   HIS A   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 2082)
  covalent geometry    : angle       0.59604 ( 2830)
  SS BOND              : bond        0.00250 (    4)
  SS BOND              : angle       1.36482 (    8)
  hydrogen bonds       : bond        0.03709 (   93)
  hydrogen bonds       : angle       4.86378 (  240)
  link_BETA1-4         : bond        0.00342 (    1)
  link_BETA1-4         : angle       1.04016 (    3)
  link_BETA1-6         : bond        0.00670 (    1)
  link_BETA1-6         : angle       1.60839 (    3)
  link_NAG-ASN         : bond        0.00115 (    1)
  link_NAG-ASN         : angle       1.42886 (    3)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.045 
Fit side-chains
REVERT: A    7 MET cc_start: 0.8016 (mtm) cc_final: 0.7788 (mtm)
REVERT: A   25 ILE cc_start: 0.8710 (mm) cc_final: 0.8362 (mt)
REVERT: A   34 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7597 (mp0)
  outliers start: 7
  outliers final: 5
  residues processed: 37
  average time/residue: 0.0495
  time to fit residues: 2.1666
Evaluate side-chains
  40 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 20 optimal weight:    0.0980
   chunk 23 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0020
   chunk 15 optimal weight:    0.2980
   chunk 0 optimal weight:    0.9980
   chunk 14 optimal weight:    0.3980
   chunk 8 optimal weight:    0.3980
   chunk 24 optimal weight:    0.1980
   chunk 12 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0470
   overall best weight:    0.1286

-------------------------------------------------------------------------------
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 = 0.3568 r_free = 0.3568 target = 0.128424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.111692 restraints weight = 3013.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.114622 restraints weight = 1679.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.116573 restraints weight = 1140.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.117818 restraints weight = 875.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.118735 restraints weight = 732.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.4407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2089  Z= 0.113
  Angle     :  0.566  10.664   2847  Z= 0.281
  Chirality :  0.041   0.130    318
  Planarity :  0.004   0.044    363
  Dihedral  :  5.598  52.499    344
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.42 %
    Favored  : 81.59 %
  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 are not related in a simple way.
  whole:  0.45 (0.54), residues: 254
  helix:  1.24 (0.58), residues: 88
  sheet: -0.28 (0.84), residues: 47
  loop : -0.04 (0.56), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 457 
 TYR   0.010   0.001   TYR B 489 
 PHE   0.007   0.001   PHE A  33 
 TRP   0.010   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 2082)
  covalent geometry    : angle       0.55969 ( 2830)
  SS BOND              : bond        0.00280 (    4)
  SS BOND              : angle       1.21908 (    8)
  hydrogen bonds       : bond        0.03300 (   93)
  hydrogen bonds       : angle       4.69171 (  240)
  link_BETA1-4         : bond        0.00382 (    1)
  link_BETA1-4         : angle       1.01380 (    3)
  link_BETA1-6         : bond        0.00674 (    1)
  link_BETA1-6         : angle       1.35892 (    3)
  link_NAG-ASN         : bond        0.00023 (    1)
  link_NAG-ASN         : angle       1.23265 (    3)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.047 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 MET cc_start: 0.7985 (mtm) cc_final: 0.7668 (mtm)
REVERT: A   25 ILE cc_start: 0.8653 (mm) cc_final: 0.8301 (mt)
  outliers start: 6
  outliers final: 6
  residues processed: 36
  average time/residue: 0.0433
  time to fit residues: 1.8683
Evaluate side-chains
  39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 23 optimal weight:    0.2980
   chunk 17 optimal weight:    0.1980
   chunk 13 optimal weight:    0.6980
   chunk 20 optimal weight:    0.4980
   chunk 2 optimal weight:    0.0570
   chunk 7 optimal weight:    0.0870
   chunk 3 optimal weight:    0.4980
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.1980
   chunk 6 optimal weight:    0.0670
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.1214

-------------------------------------------------------------------------------
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 = 0.3579 r_free = 0.3579 target = 0.129100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.112065 restraints weight = 3039.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.115028 restraints weight = 1682.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.116919 restraints weight = 1141.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.117741 restraints weight = 879.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.118901 restraints weight = 773.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.4472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   2089  Z= 0.109
  Angle     :  0.551  10.105   2847  Z= 0.275
  Chirality :  0.041   0.129    318
  Planarity :  0.004   0.044    363
  Dihedral  :  5.492  51.855    344
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.43 %
    Favored  : 82.59 %
  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 are not related in a simple way.
  whole:  0.56 (0.55), residues: 254
  helix:  1.32 (0.58), residues: 88
  sheet: -0.17 (0.85), residues: 47
  loop :  0.00 (0.57), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 457 
 TYR   0.009   0.001   TYR A  14 
 PHE   0.007   0.001   PHE A  33 
 TRP   0.008   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 2082)
  covalent geometry    : angle       0.54563 ( 2830)
  SS BOND              : bond        0.00269 (    4)
  SS BOND              : angle       1.16311 (    8)
  hydrogen bonds       : bond        0.03173 (   93)
  hydrogen bonds       : angle       4.63011 (  240)
  link_BETA1-4         : bond        0.00422 (    1)
  link_BETA1-4         : angle       0.97189 (    3)
  link_BETA1-6         : bond        0.00617 (    1)
  link_BETA1-6         : angle       1.30186 (    3)
  link_NAG-ASN         : bond        0.00004 (    1)
  link_NAG-ASN         : angle       1.20066 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 761.35 seconds
wall clock time: 13 minutes 56.20 seconds (836.20 seconds total)