Starting phenix.real_space_refine
on Tue Mar  3 11:36:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e3b_30978/03_2026/7e3b_30978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e3b_30978/03_2026/7e3b_30978.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e3b_30978/03_2026/7e3b_30978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e3b_30978/03_2026/7e3b_30978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e3b_30978/03_2026/7e3b_30978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e3b_30978/03_2026/7e3b_30978.cif"
  }
  resolution = 4.2
  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=   0.001
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      14      5.16       5
     C    2095      2.51       5
     N     541      2.21       5
     O     649      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 3299
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "B"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 941
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    Chain: "C"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 808
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98}
    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: 1.00, per 1000 atoms: 0.30
  Number of scatterers: 3299
  At special positions: 0
  Unit cell: (68.481, 85.873, 72.829, 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      14     16.00
     O     649      8.00
     N     541      7.00
     C    2095      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.04

  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 601 " - " ASN A 343 "
  Time building additional restraints: 0.20
  Conformation dependent library (CDL) restraints added in 199.5 milliseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  770

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 9 sheets defined
      11.6% alpha, 29.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 4.331A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.364A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.136A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'B' and resid 61 through 64
    Processing helix  chain 'B' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.561A  pdb=" N   SER B  35 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 11
    Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11
      removed outlier: 3.918A  pdb=" N   THR C  97 " --> pdb=" O   GLN C  90 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 49

    111 hydrogen bonds defined for protein.
    255 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: 0.48

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1049
        1.35 -     1.48: 968
        1.48 -     1.60: 1352
        1.60 -     1.73: 0
        1.73 -     1.85: 16
  Bond restraints: 3385
  Sorted by residual:
  bond pdb=" CB  PHE B  78 "
       pdb=" CG  PHE B  78 "
    ideal  model  delta    sigma   weight residual
    1.502  1.454  0.048 2.30e-02 1.89e+03 4.40e+00
  bond pdb=" N   TRP B 112 "
       pdb=" CA  TRP B 112 "
    ideal  model  delta    sigma   weight residual
    1.457  1.479 -0.022 1.29e-02 6.01e+03 2.88e+00
  bond pdb=" CD2 PHE B  78 "
       pdb=" CE2 PHE B  78 "
    ideal  model  delta    sigma   weight residual
    1.382  1.338  0.044 3.00e-02 1.11e+03 2.14e+00
  bond pdb=" CB  TRP B 112 "
       pdb=" CG  TRP B 112 "
    ideal  model  delta    sigma   weight residual
    1.498  1.453  0.045 3.10e-02 1.04e+03 2.12e+00
  bond pdb=" CB  CYS A 379 "
       pdb=" SG  CYS A 379 "
    ideal  model  delta    sigma   weight residual
    1.808  1.854 -0.046 3.30e-02 9.18e+02 1.97e+00
  ... (remaining 3380 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 4473
        2.09 -     4.17: 117
        4.17 -     6.26: 17
        6.26 -     8.35: 2
        8.35 -    10.44: 1
  Bond angle restraints: 4610
  Sorted by residual:
  angle pdb=" CA  CYS A 432 "
        pdb=" CB  CYS A 432 "
        pdb=" SG  CYS A 432 "
      ideal   model   delta    sigma   weight residual
     114.40  124.84  -10.44 2.30e+00 1.89e-01 2.06e+01
  angle pdb=" CB  LYS B  13 "
        pdb=" CG  LYS B  13 "
        pdb=" CD  LYS B  13 "
      ideal   model   delta    sigma   weight residual
     111.30  118.65   -7.35 2.30e+00 1.89e-01 1.02e+01
  angle pdb=" C   ILE C  83 "
        pdb=" N   ALA C  84 "
        pdb=" CA  ALA C  84 "
      ideal   model   delta    sigma   weight residual
     122.09  116.48    5.61 1.86e+00 2.89e-01 9.11e+00
  angle pdb=" N   CYS A 432 "
        pdb=" CA  CYS A 432 "
        pdb=" C   CYS A 432 "
      ideal   model   delta    sigma   weight residual
     108.60  112.87   -4.27 1.46e+00 4.69e-01 8.54e+00
  angle pdb=" C   GLY A 431 "
        pdb=" N   CYS A 432 "
        pdb=" CA  CYS A 432 "
      ideal   model   delta    sigma   weight residual
     121.80  116.95    4.85 1.71e+00 3.42e-01 8.04e+00
  ... (remaining 4605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 1814
       17.19 -    34.37: 147
       34.37 -    51.55: 26
       51.55 -    68.74: 7
       68.74 -    85.92: 3
  Dihedral angle restraints: 1997
    sinusoidal: 779
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.09   55.91     1      1.00e+01 1.00e-02 4.22e+01
  dihedral pdb=" CA  CYS A 432 "
           pdb=" C   CYS A 432 "
           pdb=" N   VAL A 433 "
           pdb=" CA  VAL A 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.54  -25.46     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ASP B 110 "
           pdb=" C   ASP B 110 "
           pdb=" N   ILE B 111 "
           pdb=" CA  ILE B 111 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.89  -21.11     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 1994 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 280
       0.033 -    0.066: 146
       0.066 -    0.099: 41
       0.099 -    0.132: 23
       0.132 -    0.165: 10
  Chirality restraints: 500
  Sorted by residual:
  chirality pdb=" CA  ILE C  29 "
            pdb=" N   ILE C  29 "
            pdb=" C   ILE C  29 "
            pdb=" CB  ILE C  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.81e-01
  chirality pdb=" CA  CYS A 432 "
            pdb=" N   CYS A 432 "
            pdb=" C   CYS A 432 "
            pdb=" CB  CYS A 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.56e-01
  chirality pdb=" CB  ILE B 111 "
            pdb=" CA  ILE B 111 "
            pdb=" CG1 ILE B 111 "
            pdb=" CG2 ILE B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.92e-01
  ... (remaining 497 not shown)

  Planarity restraints: 595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  34 "   -0.025 2.00e-02 2.50e+03   1.61e-02 6.50e+00
        pdb=" CG  TRP B  34 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  34 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  34 "    0.008 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  34 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  34 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  34 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  34 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B   8 "    0.027 5.00e-02 4.00e+02   4.06e-02 2.63e+00
        pdb=" N   PRO B   9 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B   9 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B   9 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  78 "    0.008 2.00e-02 2.50e+03   1.55e-02 2.40e+00
        pdb=" C   PHE B  78 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   PHE B  78 "    0.010 2.00e-02 2.50e+03
        pdb=" N   SER B  79 "    0.009 2.00e-02 2.50e+03
  ... (remaining 592 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 746
        2.77 -     3.30: 3195
        3.30 -     3.84: 5475
        3.84 -     4.37: 6437
        4.37 -     4.90: 11064
  Nonbonded interactions: 26917
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  98 "
            pdb=" N   ARG B  99 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" NH2 ARG A 346 "
            pdb=" OD2 ASP B  98 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" OD1 ASN A 450 "
            pdb=" OH  TYR B  50 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" NH2 ARG A 454 "
            pdb=" O   SER A 469 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" NH1 ARG C  18 "
            pdb=" OG1 THR C  20 "
     model   vdw
     2.296 3.120
  ... (remaining 26912 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.080
  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:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.270
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
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      :  0.006   0.048   3392  Z= 0.277
  Angle     :  0.817  10.437   4625  Z= 0.461
  Chirality :  0.049   0.165    500
  Planarity :  0.004   0.041    594
  Dihedral  : 13.333  85.922   1209
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.04 (0.38), residues: 415
  helix: -3.08 (0.86), residues: 26
  sheet: -1.07 (0.45), residues: 130
  loop : -1.32 (0.35), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  61 
 TYR   0.022   0.002   TYR A 365 
 PHE   0.019   0.002   PHE B  78 
 TRP   0.040   0.003   TRP B  34 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 ( 3385)
  covalent geometry    : angle       0.80991 ( 4610)
  SS BOND              : bond        0.00891 (    6)
  SS BOND              : angle       2.23094 (   12)
  hydrogen bonds       : bond        0.17338 (  106)
  hydrogen bonds       : angle       8.91532 (  255)
  link_NAG-ASN         : bond        0.00075 (    1)
  link_NAG-ASN         : angle       1.27390 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8499 (t70) cc_final: 0.8014 (p0)
REVERT: B   89 ASP cc_start: 0.9199 (m-30) cc_final: 0.8903 (m-30)
REVERT: B  110 ASP cc_start: 0.8839 (t0) cc_final: 0.8567 (t0)
REVERT: C   83 ILE cc_start: 0.9384 (mt) cc_final: 0.9178 (tt)
REVERT: C   88 CYS cc_start: 0.6455 (p) cc_final: 0.6036 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0676
  time to fit residues: 6.9636
Evaluate side-chains
  76 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.070387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.056847 restraints weight = 8810.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.058798 restraints weight = 5045.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.060159 restraints weight = 3479.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.061072 restraints weight = 2685.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.061765 restraints weight = 2249.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   3392  Z= 0.185
  Angle     :  0.656  10.337   4625  Z= 0.348
  Chirality :  0.047   0.159    500
  Planarity :  0.004   0.033    594
  Dihedral  :  5.658  29.170    485
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.65 (0.40), residues: 415
  helix: -2.26 (0.87), residues: 27
  sheet: -0.70 (0.47), residues: 130
  loop : -1.17 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  61 
 TYR   0.022   0.002   TYR B  53 
 PHE   0.015   0.001   PHE B  78 
 TRP   0.025   0.002   TRP B  34 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 3385)
  covalent geometry    : angle       0.64837 ( 4610)
  SS BOND              : bond        0.00842 (    6)
  SS BOND              : angle       1.99694 (   12)
  hydrogen bonds       : bond        0.03859 (  106)
  hydrogen bonds       : angle       7.18933 (  255)
  link_NAG-ASN         : bond        0.00006 (    1)
  link_NAG-ASN         : angle       1.20518 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8496 (t70) cc_final: 0.8015 (p0)
REVERT: B    2 VAL cc_start: 0.9199 (t) cc_final: 0.8969 (t)
REVERT: B   53 TYR cc_start: 0.8705 (p90) cc_final: 0.8285 (p90)
REVERT: B  110 ASP cc_start: 0.8907 (t0) cc_final: 0.8639 (t0)
REVERT: C   24 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8226 (tm-30)
REVERT: C   49 TYR cc_start: 0.8480 (p90) cc_final: 0.8219 (p90)
REVERT: C   81 GLU cc_start: 0.8656 (pp20) cc_final: 0.8452 (pp20)
REVERT: C   82 ASP cc_start: 0.8856 (m-30) cc_final: 0.8655 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0642
  time to fit residues: 7.3446
Evaluate side-chains
  82 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0020
   chunk 28 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   overall best weight:    0.5388

-------------------------------------------------------------------------------
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 = 0.2935 r_free = 0.2935 target = 0.072077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.058514 restraints weight = 8456.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.060417 restraints weight = 4954.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.061821 restraints weight = 3463.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.062740 restraints weight = 2672.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.063442 restraints weight = 2239.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3392  Z= 0.151
  Angle     :  0.631  10.215   4625  Z= 0.330
  Chirality :  0.047   0.184    500
  Planarity :  0.004   0.034    594
  Dihedral  :  5.197  27.434    485
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.54 (0.40), residues: 415
  helix: -2.27 (0.87), residues: 27
  sheet: -0.58 (0.48), residues: 132
  loop : -1.12 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.014   0.001   TYR B  53 
 PHE   0.012   0.001   PHE B  78 
 TRP   0.014   0.002   TRP B  34 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3385)
  covalent geometry    : angle       0.62396 ( 4610)
  SS BOND              : bond        0.00823 (    6)
  SS BOND              : angle       1.91200 (   12)
  hydrogen bonds       : bond        0.03370 (  106)
  hydrogen bonds       : angle       6.83129 (  255)
  link_NAG-ASN         : bond        0.00102 (    1)
  link_NAG-ASN         : angle       1.06617 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8490 (t70) cc_final: 0.7989 (p0)
REVERT: B    2 VAL cc_start: 0.9183 (t) cc_final: 0.8967 (t)
REVERT: B   37 ILE cc_start: 0.9062 (pt) cc_final: 0.8859 (pt)
REVERT: B   53 TYR cc_start: 0.8661 (p90) cc_final: 0.8284 (p90)
REVERT: B  110 ASP cc_start: 0.8815 (t0) cc_final: 0.8575 (t0)
REVERT: C   24 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8161 (tm-30)
REVERT: C   36 TYR cc_start: 0.8824 (m-80) cc_final: 0.8202 (m-80)
REVERT: C   88 CYS cc_start: 0.5751 (p) cc_final: 0.5531 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0700
  time to fit residues: 8.5466
Evaluate side-chains
  85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.070754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.057491 restraints weight = 8627.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.059428 restraints weight = 4910.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.060838 restraints weight = 3391.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.061748 restraints weight = 2600.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.062476 restraints weight = 2168.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3392  Z= 0.196
  Angle     :  0.647  10.541   4625  Z= 0.340
  Chirality :  0.047   0.200    500
  Planarity :  0.004   0.034    594
  Dihedral  :  5.132  25.006    485
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.51 (0.40), residues: 415
  helix: -2.38 (0.85), residues: 27
  sheet: -0.44 (0.48), residues: 130
  loop : -1.15 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  61 
 TYR   0.018   0.002   TYR B  52 
 PHE   0.015   0.002   PHE A 429 
 TRP   0.012   0.002   TRP B  34 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 3385)
  covalent geometry    : angle       0.63945 ( 4610)
  SS BOND              : bond        0.00909 (    6)
  SS BOND              : angle       1.90786 (   12)
  hydrogen bonds       : bond        0.03370 (  106)
  hydrogen bonds       : angle       6.62015 (  255)
  link_NAG-ASN         : bond        0.00075 (    1)
  link_NAG-ASN         : angle       1.27045 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8399 (t70) cc_final: 0.7872 (p0)
REVERT: B   53 TYR cc_start: 0.8787 (p90) cc_final: 0.8571 (p90)
REVERT: B  110 ASP cc_start: 0.8910 (t0) cc_final: 0.8707 (t0)
REVERT: C   23 CYS cc_start: 0.5332 (t) cc_final: 0.5089 (t)
REVERT: C   24 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8091 (tm-30)
REVERT: C   88 CYS cc_start: 0.6080 (p) cc_final: 0.5751 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0644
  time to fit residues: 7.4471
Evaluate side-chains
  77 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 36 optimal weight:    0.3980
   chunk 33 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.072119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.058901 restraints weight = 8540.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.060911 restraints weight = 4877.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.062330 restraints weight = 3332.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.063004 restraints weight = 2539.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.063908 restraints weight = 2177.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3392  Z= 0.159
  Angle     :  0.646  10.467   4625  Z= 0.335
  Chirality :  0.048   0.228    500
  Planarity :  0.004   0.034    594
  Dihedral  :  5.033  23.848    485
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.50 (0.40), residues: 415
  helix: -2.31 (0.89), residues: 27
  sheet: -0.41 (0.49), residues: 130
  loop : -1.16 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 466 
 TYR   0.017   0.001   TYR B  52 
 PHE   0.029   0.002   PHE B  78 
 TRP   0.015   0.002   TRP B  34 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3385)
  covalent geometry    : angle       0.63959 ( 4610)
  SS BOND              : bond        0.00852 (    6)
  SS BOND              : angle       1.87606 (   12)
  hydrogen bonds       : bond        0.03264 (  106)
  hydrogen bonds       : angle       6.58512 (  255)
  link_NAG-ASN         : bond        0.00149 (    1)
  link_NAG-ASN         : angle       1.27357 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8422 (t70) cc_final: 0.7870 (p0)
REVERT: B    2 VAL cc_start: 0.9137 (t) cc_final: 0.8881 (t)
REVERT: B   53 TYR cc_start: 0.8760 (p90) cc_final: 0.8465 (p90)
REVERT: C   23 CYS cc_start: 0.5527 (t) cc_final: 0.4478 (t)
REVERT: C   88 CYS cc_start: 0.5962 (p) cc_final: 0.5470 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0611
  time to fit residues: 7.1640
Evaluate side-chains
  79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 3 optimal weight:    0.3980
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0770
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.072289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.059204 restraints weight = 8661.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.061240 restraints weight = 4981.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.062573 restraints weight = 3407.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.063361 restraints weight = 2628.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.064200 restraints weight = 2222.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3392  Z= 0.164
  Angle     :  0.648  10.413   4625  Z= 0.336
  Chirality :  0.048   0.226    500
  Planarity :  0.004   0.034    594
  Dihedral  :  4.930  23.010    485
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.52 (0.40), residues: 415
  helix: -2.24 (0.91), residues: 27
  sheet: -0.53 (0.47), residues: 132
  loop : -1.13 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 466 
 TYR   0.016   0.001   TYR B  52 
 PHE   0.025   0.002   PHE B  78 
 TRP   0.015   0.002   TRP B 105 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 3385)
  covalent geometry    : angle       0.64148 ( 4610)
  SS BOND              : bond        0.00822 (    6)
  SS BOND              : angle       1.85055 (   12)
  hydrogen bonds       : bond        0.03184 (  106)
  hydrogen bonds       : angle       6.44463 (  255)
  link_NAG-ASN         : bond        0.00074 (    1)
  link_NAG-ASN         : angle       1.27588 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8432 (t70) cc_final: 0.7884 (p0)
REVERT: A  525 CYS cc_start: 0.6429 (m) cc_final: 0.6152 (m)
REVERT: B    2 VAL cc_start: 0.9094 (t) cc_final: 0.8827 (t)
REVERT: B   53 TYR cc_start: 0.8746 (p90) cc_final: 0.8501 (p90)
REVERT: B   81 LYS cc_start: 0.9296 (mppt) cc_final: 0.9089 (mttp)
REVERT: C   23 CYS cc_start: 0.5509 (t) cc_final: 0.4876 (t)
REVERT: C   24 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8254 (tm-30)
REVERT: C   81 GLU cc_start: 0.8502 (pp20) cc_final: 0.8246 (pp20)
REVERT: C   82 ASP cc_start: 0.8644 (m-30) cc_final: 0.8129 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0681
  time to fit residues: 8.1218
Evaluate side-chains
  80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    0.2980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.071204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.058063 restraints weight = 8832.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.059998 restraints weight = 5062.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.061376 restraints weight = 3514.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.062177 restraints weight = 2707.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.062972 restraints weight = 2287.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3392  Z= 0.183
  Angle     :  0.681  10.225   4625  Z= 0.349
  Chirality :  0.048   0.244    500
  Planarity :  0.006   0.098    594
  Dihedral  :  5.020  23.420    485
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.51 (0.39), residues: 415
  helix: -2.05 (0.94), residues: 27
  sheet: -0.56 (0.47), residues: 132
  loop : -1.12 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  61 
 TYR   0.015   0.001   TYR B  52 
 PHE   0.022   0.002   PHE B  78 
 TRP   0.012   0.002   TRP B 105 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 3385)
  covalent geometry    : angle       0.67501 ( 4610)
  SS BOND              : bond        0.00840 (    6)
  SS BOND              : angle       1.81172 (   12)
  hydrogen bonds       : bond        0.03295 (  106)
  hydrogen bonds       : angle       6.45185 (  255)
  link_NAG-ASN         : bond        0.00091 (    1)
  link_NAG-ASN         : angle       1.39815 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8442 (t70) cc_final: 0.7871 (p0)
REVERT: B    2 VAL cc_start: 0.9119 (t) cc_final: 0.8838 (t)
REVERT: B  110 ASP cc_start: 0.8716 (t0) cc_final: 0.8509 (t0)
REVERT: C    4 MET cc_start: 0.7856 (mmp) cc_final: 0.7530 (mmp)
REVERT: C   23 CYS cc_start: 0.5312 (t) cc_final: 0.4061 (t)
REVERT: C   24 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8205 (tm-30)
REVERT: C   88 CYS cc_start: 0.5990 (p) cc_final: 0.5308 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0638
  time to fit residues: 7.1271
Evaluate side-chains
  80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.2929 r_free = 0.2929 target = 0.071739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.058472 restraints weight = 8852.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.060467 restraints weight = 5079.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.061787 restraints weight = 3481.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.062845 restraints weight = 2689.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.063406 restraints weight = 2213.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3392  Z= 0.172
  Angle     :  0.699  10.048   4625  Z= 0.356
  Chirality :  0.048   0.265    500
  Planarity :  0.004   0.035    594
  Dihedral  :  4.956  23.388    485
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.45 (0.40), residues: 415
  helix: -2.18 (0.93), residues: 27
  sheet: -0.44 (0.47), residues: 132
  loop : -1.11 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 466 
 TYR   0.026   0.002   TYR B  52 
 PHE   0.019   0.001   PHE B  78 
 TRP   0.011   0.002   TRP B 105 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 3385)
  covalent geometry    : angle       0.69340 ( 4610)
  SS BOND              : bond        0.00810 (    6)
  SS BOND              : angle       1.76636 (   12)
  hydrogen bonds       : bond        0.03186 (  106)
  hydrogen bonds       : angle       6.42294 (  255)
  link_NAG-ASN         : bond        0.00112 (    1)
  link_NAG-ASN         : angle       1.41170 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8452 (t70) cc_final: 0.7845 (p0)
REVERT: B    2 VAL cc_start: 0.9084 (t) cc_final: 0.8793 (t)
REVERT: B  110 ASP cc_start: 0.8738 (t0) cc_final: 0.8521 (t0)
REVERT: C   23 CYS cc_start: 0.5412 (t) cc_final: 0.4919 (t)
REVERT: C   88 CYS cc_start: 0.5947 (p) cc_final: 0.5417 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.0682
  time to fit residues: 7.5552
Evaluate side-chains
  80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0770
   chunk 8 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0870
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.5116

-------------------------------------------------------------------------------
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 = 0.2938 r_free = 0.2938 target = 0.072284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.058431 restraints weight = 8763.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.060523 restraints weight = 4978.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.061939 restraints weight = 3407.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.062857 restraints weight = 2631.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.063664 restraints weight = 2201.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3392  Z= 0.149
  Angle     :  0.686   9.821   4625  Z= 0.347
  Chirality :  0.048   0.261    500
  Planarity :  0.004   0.035    594
  Dihedral  :  4.859  22.939    485
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.40 (0.40), residues: 415
  helix: -2.13 (0.96), residues: 27
  sheet: -0.41 (0.47), residues: 132
  loop : -1.07 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 466 
 TYR   0.025   0.001   TYR B  53 
 PHE   0.017   0.001   PHE B  78 
 TRP   0.011   0.002   TRP B 105 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3385)
  covalent geometry    : angle       0.68034 ( 4610)
  SS BOND              : bond        0.00789 (    6)
  SS BOND              : angle       1.71239 (   12)
  hydrogen bonds       : bond        0.03050 (  106)
  hydrogen bonds       : angle       6.40160 (  255)
  link_NAG-ASN         : bond        0.00138 (    1)
  link_NAG-ASN         : angle       1.30389 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8434 (t70) cc_final: 0.7813 (p0)
REVERT: B    2 VAL cc_start: 0.9076 (t) cc_final: 0.8777 (t)
REVERT: B   53 TYR cc_start: 0.8791 (p90) cc_final: 0.8394 (p90)
REVERT: C    4 MET cc_start: 0.7897 (mmp) cc_final: 0.7669 (mmp)
REVERT: C   23 CYS cc_start: 0.5370 (t) cc_final: 0.4034 (t)
REVERT: C   24 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8315 (tm-30)
REVERT: C   88 CYS cc_start: 0.5889 (p) cc_final: 0.5116 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0659
  time to fit residues: 7.1580
Evaluate side-chains
  77 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    0.0000
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    0.3980
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5584

-------------------------------------------------------------------------------
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 = 0.2931 r_free = 0.2931 target = 0.072093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.058846 restraints weight = 8764.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.060833 restraints weight = 5114.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.062137 restraints weight = 3542.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.063165 restraints weight = 2753.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.063723 restraints weight = 2283.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3392  Z= 0.159
  Angle     :  0.692   9.598   4625  Z= 0.352
  Chirality :  0.048   0.253    500
  Planarity :  0.004   0.035    594
  Dihedral  :  4.793  23.247    485
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.42 (0.40), residues: 415
  helix: -2.20 (0.97), residues: 27
  sheet: -0.42 (0.47), residues: 132
  loop : -1.09 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 466 
 TYR   0.021   0.001   TYR B  53 
 PHE   0.021   0.001   PHE B  78 
 TRP   0.012   0.002   TRP B 105 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 3385)
  covalent geometry    : angle       0.68643 ( 4610)
  SS BOND              : bond        0.00787 (    6)
  SS BOND              : angle       1.70894 (   12)
  hydrogen bonds       : bond        0.03058 (  106)
  hydrogen bonds       : angle       6.34666 (  255)
  link_NAG-ASN         : bond        0.00122 (    1)
  link_NAG-ASN         : angle       1.35813 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  452 LEU cc_start: 0.9479 (mt) cc_final: 0.9218 (mt)
REVERT: A  467 ASP cc_start: 0.8493 (t70) cc_final: 0.7848 (p0)
REVERT: B    2 VAL cc_start: 0.9046 (t) cc_final: 0.8756 (t)
REVERT: B   53 TYR cc_start: 0.8739 (p90) cc_final: 0.8342 (p90)
REVERT: C    4 MET cc_start: 0.7835 (mmp) cc_final: 0.7536 (mmp)
REVERT: C   23 CYS cc_start: 0.5338 (t) cc_final: 0.3992 (t)
REVERT: C   88 CYS cc_start: 0.5883 (p) cc_final: 0.5130 (p)
REVERT: C   93 ASN cc_start: 0.8257 (t0) cc_final: 0.7904 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0626
  time to fit residues: 6.9087
Evaluate side-chains
  76 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0970
   chunk 27 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.7578

-------------------------------------------------------------------------------
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 = 0.2919 r_free = 0.2919 target = 0.071355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.057740 restraints weight = 8811.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.059807 restraints weight = 4935.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.061155 restraints weight = 3365.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.062208 restraints weight = 2598.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.062769 restraints weight = 2138.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3392  Z= 0.189
  Angle     :  0.696   9.098   4625  Z= 0.356
  Chirality :  0.049   0.246    500
  Planarity :  0.004   0.035    594
  Dihedral  :  4.901  24.208    485
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.45 (0.40), residues: 415
  helix: -2.28 (0.95), residues: 27
  sheet: -0.44 (0.47), residues: 132
  loop : -1.09 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 466 
 TYR   0.021   0.002   TYR B  53 
 PHE   0.019   0.002   PHE B  78 
 TRP   0.010   0.002   TRP B 105 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 3385)
  covalent geometry    : angle       0.69062 ( 4610)
  SS BOND              : bond        0.00784 (    6)
  SS BOND              : angle       1.66191 (   12)
  hydrogen bonds       : bond        0.03171 (  106)
  hydrogen bonds       : angle       6.36896 (  255)
  link_NAG-ASN         : bond        0.00091 (    1)
  link_NAG-ASN         : angle       1.54197 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 817.91 seconds
wall clock time: 14 minutes 42.72 seconds (882.72 seconds total)