Starting phenix.real_space_refine
on Fri Aug 22 14:08:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zqq_60388/08_2025/8zqq_60388.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zqq_60388/08_2025/8zqq_60388.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zqq_60388/08_2025/8zqq_60388.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zqq_60388/08_2025/8zqq_60388.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zqq_60388/08_2025/8zqq_60388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zqq_60388/08_2025/8zqq_60388.map"
  }
  resolution = 2.5
  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=  -0.002 sd=   0.101
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: 6
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     Cl      1      4.86       5
     Na      1      4.78       5
     C    2559      2.51       5
     N     575      2.21       5
     O     680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3836
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3788
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 469}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 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
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 9
          Unusual residues: {' CL': 1, ' NA': 1, 'CHT': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.18, per 1000 atoms: 0.31
  Number of scatterers: 3836
  At special positions: 0
  Unit cell: (87.55, 67.15, 87.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      20     16.00
     Na      1     11.00
     O     680      8.00
     N     575      7.00
     C    2559      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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 B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 301 "
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 151.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  896

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 1 sheets defined
      77.8% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 29
    Processing helix  chain 'A' and resid 50 through 63
    Processing helix  chain 'A' and resid 64 through 77
      removed outlier: 3.806A  pdb=" N   ILE A  68 " --> pdb=" O   GLY A  64 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   THR A  71 " --> pdb=" O   TYR A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 102
      removed outlier: 3.715A  pdb=" N   SER A  92 " --> pdb=" O   PRO A  88 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU A  95 " --> pdb=" O   TYR A  91 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A  96 " --> pdb=" O   SER A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 122
    Processing helix  chain 'A' and resid 123 through 158
      removed outlier: 4.026A  pdb=" N   ILE A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      Proline residue:  A 133  - end of helix
    Processing helix  chain 'A' and resid 160 through 180
      removed outlier: 3.586A  pdb=" N   GLY A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 201
    Processing helix  chain 'A' and resid 202 through 208
    Processing helix  chain 'A' and resid 214 through 222
      removed outlier: 4.524A  pdb=" N   VAL A 220 " --> pdb=" O   GLY A 216 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ALA A 222 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 251
      removed outlier: 3.544A  pdb=" N   GLY A 251 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 263
      removed outlier: 3.876A  pdb=" N   ARG A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 297
      removed outlier: 4.044A  pdb=" N   ILE A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      Proline residue:  A 287  - end of helix
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 6.178A  pdb=" N   ASN A 301 " --> pdb=" O   THR A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 317
      No H-bonds generated for 'chain 'A' and resid 315 through 317'
    Processing helix  chain 'A' and resid 318 through 327
    Processing helix  chain 'A' and resid 329 through 363
      removed outlier: 4.023A  pdb=" N   SER A 350 " --> pdb=" O   SER A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 399
    Processing helix  chain 'A' and resid 402 through 409
    Processing helix  chain 'A' and resid 410 through 427
      removed outlier: 4.404A  pdb=" N   PHE A 418 " --> pdb=" O   TYR A 414 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 431 through 450
      removed outlier: 3.938A  pdb=" N   GLY A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 503
      removed outlier: 3.635A  pdb=" N   LEU A 482 " --> pdb=" O   PRO A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 512
    Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467

    270 hydrogen bonds defined for protein.
    795 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: 0.58

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1109
        1.34 -     1.46: 822
        1.46 -     1.58: 1975
        1.58 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 3941
  Sorted by residual:
  bond pdb=" CA  LYS A 104 "
       pdb=" C   LYS A 104 "
    ideal  model  delta    sigma   weight residual
    1.524  1.561 -0.038 1.26e-02 6.30e+03 8.86e+00
  bond pdb=" C   LYS A 104 "
       pdb=" N   PRO A 105 "
    ideal  model  delta    sigma   weight residual
    1.335  1.367 -0.033 1.19e-02 7.06e+03 7.64e+00
  bond pdb=" C   PRO A 508 "
       pdb=" N   PRO A 509 "
    ideal  model  delta    sigma   weight residual
    1.335  1.367 -0.033 1.19e-02 7.06e+03 7.58e+00
  bond pdb=" C   GLU A 451 "
       pdb=" N   PRO A 452 "
    ideal  model  delta    sigma   weight residual
    1.336  1.366 -0.030 1.25e-02 6.40e+03 5.78e+00
  bond pdb=" C1  BMA B   3 "
       pdb=" C2  BMA B   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.551 -0.032 2.00e-02 2.50e+03 2.58e+00
  ... (remaining 3936 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 5269
        1.85 -     3.70: 87
        3.70 -     5.56: 20
        5.56 -     7.41: 3
        7.41 -     9.26: 5
  Bond angle restraints: 5384
  Sorted by residual:
  angle pdb=" N   THR A 506 "
        pdb=" CA  THR A 506 "
        pdb=" C   THR A 506 "
      ideal   model   delta    sigma   weight residual
     108.67  100.65    8.02 1.67e+00 3.59e-01 2.31e+01
  angle pdb=" N   LEU A 507 "
        pdb=" CA  LEU A 507 "
        pdb=" C   LEU A 507 "
      ideal   model   delta    sigma   weight residual
     109.58  117.00   -7.42 1.75e+00 3.27e-01 1.80e+01
  angle pdb=" C   GLU A 451 "
        pdb=" N   PRO A 452 "
        pdb=" CA  PRO A 452 "
      ideal   model   delta    sigma   weight residual
     119.56  115.72    3.84 1.01e+00 9.80e-01 1.44e+01
  angle pdb=" CA  THR A 506 "
        pdb=" C   THR A 506 "
        pdb=" N   LEU A 507 "
      ideal   model   delta    sigma   weight residual
     119.98  116.81    3.17 8.50e-01 1.38e+00 1.39e+01
  angle pdb=" C   PRO A 508 "
        pdb=" N   PRO A 509 "
        pdb=" CA  PRO A 509 "
      ideal   model   delta    sigma   weight residual
     119.56  116.54    3.02 1.02e+00 9.61e-01 8.78e+00
  ... (remaining 5379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.90: 2103
       21.90 -    43.80: 132
       43.80 -    65.70: 23
       65.70 -    87.60: 11
       87.60 -   109.50: 4
  Dihedral angle restraints: 2273
    sinusoidal: 858
      harmonic: 1415
  Sorted by residual:
  dihedral pdb=" CA  THR A 312 "
           pdb=" C   THR A 312 "
           pdb=" N   THR A 313 "
           pdb=" CA  THR A 313 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.74   19.26     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" O4  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  179.21  109.50     1      3.00e+01 1.11e-03 1.42e+01
  dihedral pdb=" CA  TRP A 228 "
           pdb=" C   TRP A 228 "
           pdb=" N   LEU A 229 "
           pdb=" CA  LEU A 229 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.34   18.66     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 2270 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 525
       0.056 -    0.111: 99
       0.111 -    0.166: 8
       0.166 -    0.222: 1
       0.222 -    0.277: 1
  Chirality restraints: 634
  Sorted by residual:
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  LEU A 507 "
            pdb=" N   LEU A 507 "
            pdb=" C   LEU A 507 "
            pdb=" CB  LEU A 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.16e-01
  chirality pdb=" CA  PRO A 509 "
            pdb=" N   PRO A 509 "
            pdb=" C   PRO A 509 "
            pdb=" CB  PRO A 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.65e-01
  ... (remaining 631 not shown)

  Planarity restraints: 649
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 309 "   -0.022 5.00e-02 4.00e+02   3.26e-02 1.71e+00
        pdb=" N   PRO A 310 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 310 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 310 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 508 "    0.007 2.00e-02 2.50e+03   1.29e-02 1.68e+00
        pdb=" C   PRO A 508 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   PRO A 508 "    0.008 2.00e-02 2.50e+03
        pdb=" N   PRO A 509 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 359 "    0.006 2.00e-02 2.50e+03   1.26e-02 1.58e+00
        pdb=" C   PHE A 359 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   PHE A 359 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ALA A 360 "    0.007 2.00e-02 2.50e+03
  ... (remaining 646 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 409
        2.75 -     3.29: 3687
        3.29 -     3.82: 6399
        3.82 -     4.36: 7322
        4.36 -     4.90: 12990
  Nonbonded interactions: 30807
  Sorted by model distance:
  nonbonded pdb=" O   VAL A  63 "
            pdb="NA    NA A 602 "
     model   vdw
     2.211 2.470
  nonbonded pdb=" OG  SER A 346 "
            pdb="NA    NA A 602 "
     model   vdw
     2.257 2.470
  nonbonded pdb=" OE2 GLU A 138 "
            pdb=" OG  SER A 354 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OD1 ASP A 242 "
            pdb=" OG1 THR A 481 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   ALA A  60 "
            pdb="NA    NA A 602 "
     model   vdw
     2.323 2.470
  ... (remaining 30802 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.980
  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:6.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3944  Z= 0.184
  Angle     :  0.654   9.262   5393  Z= 0.342
  Chirality :  0.042   0.277    634
  Planarity :  0.004   0.033    648
  Dihedral  : 16.305 109.502   1377
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 11.81 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.39), residues: 486
  helix:  1.89 (0.28), residues: 358
  sheet: -2.57 (1.51), residues: 10
  loop : -0.69 (0.60), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 382 
 TYR   0.012   0.001   TYR A 496 
 PHE   0.008   0.001   PHE A 488 
 TRP   0.012   0.001   TRP A 228 
 HIS   0.002   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3941)
  covalent geometry    : angle       0.65193 ( 5384)
  hydrogen bonds       : bond        0.14081 (  270)
  hydrogen bonds       : angle       5.05999 (  795)
  link_BETA1-4         : bond        0.00561 (    2)
  link_BETA1-4         : angle       1.48506 (    6)
  link_NAG-ASN         : bond        0.00332 (    1)
  link_NAG-ASN         : angle       1.31020 (    3)

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

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

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  263 SER cc_start: 0.7881 (m) cc_final: 0.7486 (p)
REVERT: A  451 GLU cc_start: 0.8464 (tp30) cc_final: 0.8197 (tp30)
  outliers start: 1
  outliers final: 1
  residues processed: 52
  average time/residue: 0.5832
  time to fit residues: 31.3509
Evaluate side-chains
  50 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.1980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.121833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.094584 restraints weight = 4047.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.68
r_work: 0.2920 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.0527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3944  Z= 0.148
  Angle     :  0.569   6.727   5393  Z= 0.300
  Chirality :  0.040   0.149    634
  Planarity :  0.005   0.037    648
  Dihedral  :  9.241  68.386    591
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 11.06 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.39), residues: 486
  helix:  2.04 (0.27), residues: 359
  sheet: -2.35 (1.47), residues: 10
  loop : -1.06 (0.59), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 369 
 TYR   0.012   0.001   TYR A 496 
 PHE   0.009   0.001   PHE A 488 
 TRP   0.011   0.001   TRP A 228 
 HIS   0.002   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3941)
  covalent geometry    : angle       0.56425 ( 5384)
  hydrogen bonds       : bond        0.06874 (  270)
  hydrogen bonds       : angle       4.15058 (  795)
  link_BETA1-4         : bond        0.00653 (    2)
  link_BETA1-4         : angle       2.15852 (    6)
  link_NAG-ASN         : bond        0.00248 (    1)
  link_NAG-ASN         : angle       1.12837 (    3)

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

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

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  174 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7455 (mp)
REVERT: A  263 SER cc_start: 0.7968 (m) cc_final: 0.7617 (p)
REVERT: A  318 MET cc_start: 0.8187 (mtt) cc_final: 0.7843 (mtm)
  outliers start: 4
  outliers final: 2
  residues processed: 50
  average time/residue: 0.5786
  time to fit residues: 29.9184
Evaluate side-chains
  49 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  178 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 16 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0470
   chunk 19 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.3676

-------------------------------------------------------------------------------
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 = 0.3449 r_free = 0.3449 target = 0.126338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.099338 restraints weight = 4001.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 1.67
r_work: 0.2993 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.0777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3944  Z= 0.121
  Angle     :  0.511   5.963   5393  Z= 0.266
  Chirality :  0.039   0.135    634
  Planarity :  0.004   0.037    648
  Dihedral  :  6.139  36.651    591
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 10.30 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.40), residues: 486
  helix:  2.30 (0.27), residues: 359
  sheet: -2.13 (1.47), residues: 10
  loop : -0.97 (0.60), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 369 
 TYR   0.010   0.001   TYR A 496 
 PHE   0.009   0.001   PHE A 217 
 TRP   0.011   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 3941)
  covalent geometry    : angle       0.50600 ( 5384)
  hydrogen bonds       : bond        0.05395 (  270)
  hydrogen bonds       : angle       3.97133 (  795)
  link_BETA1-4         : bond        0.00577 (    2)
  link_BETA1-4         : angle       2.21013 (    6)
  link_NAG-ASN         : bond        0.00481 (    1)
  link_NAG-ASN         : angle       0.88909 (    3)

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

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

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7349 (mttt)
REVERT: A  174 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7469 (mp)
REVERT: A  263 SER cc_start: 0.7876 (m) cc_final: 0.7546 (p)
REVERT: A  318 MET cc_start: 0.8018 (mtt) cc_final: 0.7777 (mtm)
  outliers start: 7
  outliers final: 2
  residues processed: 51
  average time/residue: 0.5403
  time to fit residues: 28.5290
Evaluate side-chains
  49 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  174 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3398 r_free = 0.3398 target = 0.122129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.094844 restraints weight = 3987.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 1.67
r_work: 0.2925 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.0741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3944  Z= 0.145
  Angle     :  0.547   6.146   5393  Z= 0.290
  Chirality :  0.040   0.151    634
  Planarity :  0.004   0.051    648
  Dihedral  :  5.059  36.389    591
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.31 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.39), residues: 486
  helix:  2.21 (0.27), residues: 359
  sheet: -2.15 (1.46), residues: 10
  loop : -0.95 (0.59), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 260 
 TYR   0.012   0.001   TYR A 496 
 PHE   0.010   0.001   PHE A 502 
 TRP   0.009   0.001   TRP A 228 
 HIS   0.002   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3941)
  covalent geometry    : angle       0.54342 ( 5384)
  hydrogen bonds       : bond        0.06666 (  270)
  hydrogen bonds       : angle       4.01992 (  795)
  link_BETA1-4         : bond        0.00616 (    2)
  link_BETA1-4         : angle       1.92755 (    6)
  link_NAG-ASN         : bond        0.00444 (    1)
  link_NAG-ASN         : angle       0.92069 (    3)

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

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

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  174 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7441 (mp)
REVERT: A  263 SER cc_start: 0.8054 (m) cc_final: 0.7759 (p)
REVERT: A  318 MET cc_start: 0.8245 (mtt) cc_final: 0.7927 (mtm)
  outliers start: 5
  outliers final: 2
  residues processed: 50
  average time/residue: 0.5346
  time to fit residues: 27.7298
Evaluate side-chains
  50 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  178 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0870
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    0.2980
   chunk 2 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.3401 r_free = 0.3401 target = 0.122973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.095721 restraints weight = 4031.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.68
r_work: 0.2951 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.0783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3944  Z= 0.131
  Angle     :  0.522   7.611   5393  Z= 0.276
  Chirality :  0.039   0.146    634
  Planarity :  0.004   0.049    648
  Dihedral  :  4.721  31.572    591
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.06 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.39), residues: 486
  helix:  2.29 (0.27), residues: 359
  sheet: -1.98 (1.47), residues: 10
  loop : -0.99 (0.60), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 107 
 TYR   0.011   0.001   TYR A 496 
 PHE   0.008   0.001   PHE A 502 
 TRP   0.010   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3941)
  covalent geometry    : angle       0.51915 ( 5384)
  hydrogen bonds       : bond        0.06030 (  270)
  hydrogen bonds       : angle       3.97008 (  795)
  link_BETA1-4         : bond        0.00612 (    2)
  link_BETA1-4         : angle       1.61802 (    6)
  link_NAG-ASN         : bond        0.00500 (    1)
  link_NAG-ASN         : angle       0.82539 (    3)

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

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

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   67 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.7559 (m-80)
REVERT: A  174 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7502 (mp)
REVERT: A  259 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: A  263 SER cc_start: 0.7999 (m) cc_final: 0.7671 (p)
REVERT: A  318 MET cc_start: 0.8132 (mtt) cc_final: 0.7880 (mtm)
  outliers start: 7
  outliers final: 4
  residues processed: 50
  average time/residue: 0.5282
  time to fit residues: 27.3073
Evaluate side-chains
  50 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  178 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3389 r_free = 0.3389 target = 0.121452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.094045 restraints weight = 4049.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 1.69
r_work: 0.2914 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.0819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3944  Z= 0.149
  Angle     :  0.556   7.314   5393  Z= 0.296
  Chirality :  0.040   0.154    634
  Planarity :  0.004   0.049    648
  Dihedral  :  4.783  28.374    591
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.31 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.39), residues: 486
  helix:  2.18 (0.27), residues: 359
  sheet: -2.12 (1.44), residues: 10
  loop : -1.00 (0.59), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 382 
 TYR   0.012   0.001   TYR A 496 
 PHE   0.011   0.001   PHE A 502 
 TRP   0.009   0.001   TRP A 228 
 HIS   0.001   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3941)
  covalent geometry    : angle       0.55407 ( 5384)
  hydrogen bonds       : bond        0.06821 (  270)
  hydrogen bonds       : angle       4.01702 (  795)
  link_BETA1-4         : bond        0.00611 (    2)
  link_BETA1-4         : angle       1.46290 (    6)
  link_NAG-ASN         : bond        0.00454 (    1)
  link_NAG-ASN         : angle       0.81771 (    3)

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

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

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A  174 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7392 (mp)
REVERT: A  263 SER cc_start: 0.8073 (m) cc_final: 0.7786 (p)
  outliers start: 7
  outliers final: 5
  residues processed: 50
  average time/residue: 0.5426
  time to fit residues: 28.0306
Evaluate side-chains
  51 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  178 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3401 r_free = 0.3401 target = 0.122372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.095069 restraints weight = 4039.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.69
r_work: 0.2929 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.0831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3944  Z= 0.139
  Angle     :  0.540   6.982   5393  Z= 0.287
  Chirality :  0.039   0.150    634
  Planarity :  0.004   0.050    648
  Dihedral  :  4.712  29.213    591
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.06 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.39), residues: 486
  helix:  2.22 (0.27), residues: 359
  sheet: -2.02 (1.45), residues: 10
  loop : -0.93 (0.60), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 107 
 TYR   0.012   0.001   TYR A 496 
 PHE   0.010   0.001   PHE A 502 
 TRP   0.010   0.001   TRP A 228 
 HIS   0.001   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3941)
  covalent geometry    : angle       0.53776 ( 5384)
  hydrogen bonds       : bond        0.06405 (  270)
  hydrogen bonds       : angle       3.99069 (  795)
  link_BETA1-4         : bond        0.00606 (    2)
  link_BETA1-4         : angle       1.40233 (    6)
  link_NAG-ASN         : bond        0.00452 (    1)
  link_NAG-ASN         : angle       0.81205 (    3)

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

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

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   67 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.7575 (m-80)
REVERT: A  174 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7421 (mp)
REVERT: A  259 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8195 (tm-30)
REVERT: A  263 SER cc_start: 0.8052 (m) cc_final: 0.7724 (p)
REVERT: A  318 MET cc_start: 0.8215 (mtt) cc_final: 0.7851 (mtm)
  outliers start: 7
  outliers final: 5
  residues processed: 51
  average time/residue: 0.5342
  time to fit residues: 28.2732
Evaluate side-chains
  52 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  178 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0050
   chunk 39 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.5194

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.123987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.096776 restraints weight = 4028.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 1.69
r_work: 0.2954 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.0872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3944  Z= 0.129
  Angle     :  0.523   6.505   5393  Z= 0.277
  Chirality :  0.039   0.140    634
  Planarity :  0.004   0.050    648
  Dihedral  :  4.551  28.889    591
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.81 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.39), residues: 486
  helix:  2.28 (0.27), residues: 359
  sheet: -1.94 (1.48), residues: 10
  loop : -0.85 (0.61), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 260 
 TYR   0.011   0.001   TYR A 496 
 PHE   0.009   0.001   PHE A 502 
 TRP   0.011   0.001   TRP A 228 
 HIS   0.001   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3941)
  covalent geometry    : angle       0.52073 ( 5384)
  hydrogen bonds       : bond        0.05883 (  270)
  hydrogen bonds       : angle       3.93426 (  795)
  link_BETA1-4         : bond        0.00582 (    2)
  link_BETA1-4         : angle       1.35565 (    6)
  link_NAG-ASN         : bond        0.00466 (    1)
  link_NAG-ASN         : angle       0.75603 (    3)

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

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

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A   67 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.7591 (m-80)
REVERT: A  174 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7437 (mp)
REVERT: A  259 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: A  263 SER cc_start: 0.7979 (m) cc_final: 0.7649 (p)
REVERT: A  318 MET cc_start: 0.8037 (mtt) cc_final: 0.7749 (mtm)
REVERT: A  451 GLU cc_start: 0.8559 (tp30) cc_final: 0.8284 (tp30)
  outliers start: 8
  outliers final: 5
  residues processed: 51
  average time/residue: 0.5259
  time to fit residues: 27.7232
Evaluate side-chains
  53 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  178 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0040
   chunk 39 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.123417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.096198 restraints weight = 4016.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 1.68
r_work: 0.2957 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.0926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3944  Z= 0.129
  Angle     :  0.525   6.448   5393  Z= 0.277
  Chirality :  0.039   0.143    634
  Planarity :  0.005   0.067    648
  Dihedral  :  4.495  29.229    591
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.56 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.39), residues: 486
  helix:  2.28 (0.27), residues: 359
  sheet: -1.96 (1.47), residues: 10
  loop : -0.85 (0.60), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 260 
 TYR   0.011   0.001   TYR A 496 
 PHE   0.009   0.001   PHE A 502 
 TRP   0.010   0.001   TRP A 228 
 HIS   0.001   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 3941)
  covalent geometry    : angle       0.52283 ( 5384)
  hydrogen bonds       : bond        0.05865 (  270)
  hydrogen bonds       : angle       3.91732 (  795)
  link_BETA1-4         : bond        0.00591 (    2)
  link_BETA1-4         : angle       1.32016 (    6)
  link_NAG-ASN         : bond        0.00432 (    1)
  link_NAG-ASN         : angle       0.75047 (    3)

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

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

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A   67 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.7592 (m-80)
REVERT: A  174 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7433 (mp)
REVERT: A  259 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8264 (tm-30)
REVERT: A  263 SER cc_start: 0.7967 (m) cc_final: 0.7631 (p)
  outliers start: 8
  outliers final: 5
  residues processed: 51
  average time/residue: 0.5516
  time to fit residues: 29.0990
Evaluate side-chains
  51 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  178 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 39 optimal weight:    0.1980
   chunk 41 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 29 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3411 r_free = 0.3411 target = 0.123783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.096424 restraints weight = 4094.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 1.70
r_work: 0.2960 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.0921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3944  Z= 0.128
  Angle     :  0.524   6.341   5393  Z= 0.276
  Chirality :  0.039   0.142    634
  Planarity :  0.005   0.060    648
  Dihedral  :  4.443  29.211    591
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.81 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.39), residues: 486
  helix:  2.30 (0.27), residues: 359
  sheet: -1.98 (1.46), residues: 10
  loop : -0.82 (0.61), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 260 
 TYR   0.011   0.001   TYR A 496 
 PHE   0.008   0.001   PHE A 502 
 TRP   0.011   0.001   TRP A 228 
 HIS   0.001   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3941)
  covalent geometry    : angle       0.52258 ( 5384)
  hydrogen bonds       : bond        0.05772 (  270)
  hydrogen bonds       : angle       3.90738 (  795)
  link_BETA1-4         : bond        0.00585 (    2)
  link_BETA1-4         : angle       1.29385 (    6)
  link_NAG-ASN         : bond        0.00416 (    1)
  link_NAG-ASN         : angle       0.74537 (    3)

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

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

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  972 Ramachandran restraints generated.
    486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A   67 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.7601 (m-80)
REVERT: A  174 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7429 (mp)
REVERT: A  259 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8268 (tm-30)
REVERT: A  263 SER cc_start: 0.7953 (m) cc_final: 0.7611 (p)
  outliers start: 7
  outliers final: 5
  residues processed: 49
  average time/residue: 0.5059
  time to fit residues: 25.7765
Evaluate side-chains
  52 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  178 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 29 optimal weight:    0.4980
   chunk 48 optimal weight:    0.0060
   chunk 18 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0770
   chunk 47 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.3954

-------------------------------------------------------------------------------
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 = 0.3454 r_free = 0.3454 target = 0.126809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.099751 restraints weight = 3976.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.68
r_work: 0.2998 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3944  Z= 0.118
  Angle     :  0.502   6.050   5393  Z= 0.263
  Chirality :  0.038   0.136    634
  Planarity :  0.004   0.056    648
  Dihedral  :  4.265  25.815    591
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.31 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.36 (0.39), residues: 486
  helix:  2.36 (0.27), residues: 360
  sheet: -1.86 (1.52), residues: 10
  loop : -0.72 (0.62), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 260 
 TYR   0.009   0.001   TYR A 496 
 PHE   0.008   0.001   PHE A 217 
 TRP   0.011   0.001   TRP A 228 
 HIS   0.001   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 3941)
  covalent geometry    : angle       0.50070 ( 5384)
  hydrogen bonds       : bond        0.05161 (  270)
  hydrogen bonds       : angle       3.85758 (  795)
  link_BETA1-4         : bond        0.00574 (    2)
  link_BETA1-4         : angle       1.27868 (    6)
  link_NAG-ASN         : bond        0.00431 (    1)
  link_NAG-ASN         : angle       0.68618 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1598.44 seconds
wall clock time: 27 minutes 56.68 seconds (1676.68 seconds total)