Starting phenix.real_space_refine
on Fri Aug 22 13:45:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i3u_35156/08_2025/8i3u_35156.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i3u_35156/08_2025/8i3u_35156.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i3u_35156/08_2025/8i3u_35156.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i3u_35156/08_2025/8i3u_35156.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i3u_35156/08_2025/8i3u_35156.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i3u_35156/08_2025/8i3u_35156.cif"
  }
  resolution = 3.6
  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=   0.036
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      16      5.16       5
     C    2161      2.51       5
     N     579      2.21       5
     O     652      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3408
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1552
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
    Chain: "H"
      Number of atoms: 1028
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1028
          Classifications: {'peptide': 133}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 128}
    Chain: "L"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 814
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 7, 'TRANS': 100}
    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: 1.15, per 1000 atoms: 0.34
  Number of scatterers: 3408
  At special positions: 0
  Unit cell: (63.65, 61.75, 106.4, 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      16     16.00
     O     652      8.00
     N     579      7.00
     C    2161      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.39
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
  Time building additional restraints: 0.30
  Conformation dependent library (CDL) restraints added in 127.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 9 sheets defined
      10.3% alpha, 25.4% 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 337 through 343
      removed outlier: 3.575A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.117A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.339A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.644A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.551A  pdb=" N   ILE H  87 " --> pdb=" O   SER H  84 " (cutoff:3.500A)
    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 'H' and resid 3 through 7
      removed outlier: 3.525A  pdb=" N   THR H  68 " --> pdb=" O   GLN H  81 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.614A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   LEU H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   MET H  34 " --> pdb=" O   LEU H  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 99
    Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.427A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    102 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: 0.47

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1100
        1.34 -     1.46: 903
        1.46 -     1.58: 1473
        1.58 -     1.70: 0
        1.70 -     1.81: 20
  Bond restraints: 3496
  Sorted by residual:
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.91e+00
  bond pdb=" N   PRO L  95A"
       pdb=" CA  PRO L  95A"
    ideal  model  delta    sigma   weight residual
    1.469  1.484 -0.015 1.28e-02 6.10e+03 1.42e+00
  bond pdb=" C5  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.23e+00
  bond pdb=" C3  NAG A1301 "
       pdb=" O3  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 1.03e+00
  bond pdb=" CA  ILE A 410 "
       pdb=" CB  ILE A 410 "
    ideal  model  delta    sigma   weight residual
    1.527  1.538 -0.012 1.31e-02 5.83e+03 7.90e-01
  ... (remaining 3491 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 4629
        1.35 -     2.71: 89
        2.71 -     4.06: 22
        4.06 -     5.41: 8
        5.41 -     6.76: 1
  Bond angle restraints: 4749
  Sorted by residual:
  angle pdb=" C   PRO L  95 "
        pdb=" N   PRO L  95A"
        pdb=" CA  PRO L  95A"
      ideal   model   delta    sigma   weight residual
     119.84  113.08    6.76 1.25e+00 6.40e-01 2.93e+01
  angle pdb=" N   PRO L  95 "
        pdb=" CA  PRO L  95 "
        pdb=" C   PRO L  95 "
      ideal   model   delta    sigma   weight residual
     110.70  114.12   -3.42 1.22e+00 6.72e-01 7.84e+00
  angle pdb=" CA  PRO L  95 "
        pdb=" C   PRO L  95 "
        pdb=" N   PRO L  95A"
      ideal   model   delta    sigma   weight residual
     117.93  120.61   -2.68 1.20e+00 6.94e-01 4.98e+00
  angle pdb=" C   VAL H  48 "
        pdb=" N   SER H  49 "
        pdb=" CA  SER H  49 "
      ideal   model   delta    sigma   weight residual
     122.21  118.76    3.45 1.62e+00 3.81e-01 4.53e+00
  angle pdb=" C   GLY A 476 "
        pdb=" N   SER A 477 "
        pdb=" CA  SER A 477 "
      ideal   model   delta    sigma   weight residual
     121.54  125.09   -3.55 1.91e+00 2.74e-01 3.46e+00
  ... (remaining 4744 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.54: 1865
       11.54 -    23.08: 136
       23.08 -    34.61: 46
       34.61 -    46.15: 10
       46.15 -    57.69: 2
  Dihedral angle restraints: 2059
    sinusoidal: 812
      harmonic: 1247
  Sorted by residual:
  dihedral pdb=" CA  PRO L  95 "
           pdb=" C   PRO L  95 "
           pdb=" N   PRO L  95A"
           pdb=" CA  PRO L  95A"
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.73   20.27     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  TYR H  91 "
           pdb=" C   TYR H  91 "
           pdb=" N   CYS H  92 "
           pdb=" CA  CYS H  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.04   18.96     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  118.67  -25.67     1      1.00e+01 1.00e-02 9.48e+00
  ... (remaining 2056 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 301
       0.027 -    0.053: 126
       0.053 -    0.080: 29
       0.080 -    0.106: 37
       0.106 -    0.132: 12
  Chirality restraints: 505
  Sorted by residual:
  chirality pdb=" CA  ILE A 434 "
            pdb=" N   ILE A 434 "
            pdb=" C   ILE A 434 "
            pdb=" CB  ILE A 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  GLU H  26 "
            pdb=" N   GLU H  26 "
            pdb=" C   GLU H  26 "
            pdb=" CB  GLU H  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.71e-01
  chirality pdb=" CA  VAL A 382 "
            pdb=" N   VAL A 382 "
            pdb=" C   VAL A 382 "
            pdb=" CB  VAL A 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.64e-01
  ... (remaining 502 not shown)

  Planarity restraints: 621
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L  95 "   -0.058 5.00e-02 4.00e+02   8.78e-02 1.23e+01
        pdb=" N   PRO L  95A"    0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO L  95A"   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO L  95A"   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP L  94 "    0.030 5.00e-02 4.00e+02   4.60e-02 3.38e+00
        pdb=" N   PRO L  95 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO L  95 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO L  95 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 490 "    0.018 5.00e-02 4.00e+02   2.73e-02 1.20e+00
        pdb=" N   PRO A 491 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 491 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 491 "    0.015 5.00e-02 4.00e+02
  ... (remaining 618 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 221
        2.74 -     3.28: 3219
        3.28 -     3.82: 5418
        3.82 -     4.36: 6360
        4.36 -     4.90: 11589
  Nonbonded interactions: 26807
  Sorted by model distance:
  nonbonded pdb=" O   HIS L  49 "
            pdb=" OG1 THR L  53 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OD2 ASP A 398 "
            pdb=" OH  TYR A 423 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" NZ  LYS A 417 "
            pdb=" OD2 ASP H  31 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" O   ILE H  29 "
            pdb=" NH2 ARG H  71 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" NH2 ARG A 454 "
            pdb=" O   SER A 469 "
     model   vdw
     2.319 3.120
  ... (remaining 26802 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:             6.620
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.470
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
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      :  0.007   0.363   3502  Z= 0.331
  Angle     :  0.641  23.216   4762  Z= 0.343
  Chirality :  0.041   0.132    505
  Planarity :  0.005   0.088    620
  Dihedral  :  9.198  57.687   1258
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  5.72 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.41), residues: 431
  helix: -1.62 (0.94), residues: 27
  sheet:  0.02 (0.46), residues: 132
  loop : -0.34 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  18 
 TYR   0.011   0.001   TYR L  91 
 PHE   0.006   0.001   PHE A 456 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 3496)
  covalent geometry    : angle       0.53518 ( 4749)
  SS BOND              : bond        0.16245 (    5)
  SS BOND              : angle       7.71965 (   10)
  hydrogen bonds       : bond        0.17501 (  102)
  hydrogen bonds       : angle       9.43176 (  255)
  link_NAG-ASN         : bond        0.00215 (    1)
  link_NAG-ASN         : angle       0.96077 (    3)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A  392 PHE cc_start: 0.7569 (m-80) cc_final: 0.7264 (m-80)
REVERT: A  444 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8073 (mtmm)
REVERT: H   34 MET cc_start: 0.8171 (mmm) cc_final: 0.7867 (mmm)
REVERT: L   29 ILE cc_start: 0.7289 (mm) cc_final: 0.7057 (mm)
  outliers start: 4
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0668
  time to fit residues: 9.0302
Evaluate side-chains
  81 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0970
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 100 ASN
L  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.156940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.131612 restraints weight = 4483.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.135402 restraints weight = 2715.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.138019 restraints weight = 1963.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.139754 restraints weight = 1556.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.140697 restraints weight = 1325.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3502  Z= 0.179
  Angle     :  0.597   8.475   4762  Z= 0.305
  Chirality :  0.043   0.154    505
  Planarity :  0.006   0.090    620
  Dihedral  :  4.953  26.093    505
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 14.44 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.49 (0.41), residues: 431
  helix: -1.37 (0.99), residues: 28
  sheet:  0.22 (0.47), residues: 130
  loop : -0.44 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 100J
 TYR   0.018   0.001   TYR L  91 
 PHE   0.014   0.001   PHE A 342 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 3496)
  covalent geometry    : angle       0.59507 ( 4749)
  SS BOND              : bond        0.00459 (    5)
  SS BOND              : angle       1.03303 (   10)
  hydrogen bonds       : bond        0.03670 (  102)
  hydrogen bonds       : angle       6.97629 (  255)
  link_NAG-ASN         : bond        0.00198 (    1)
  link_NAG-ASN         : angle       0.96611 (    3)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7867 (m-80) cc_final: 0.7640 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 94
  average time/residue: 0.0886
  time to fit residues: 9.7665
Evaluate side-chains
  90 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   56 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  102 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0670
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.168596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.142770 restraints weight = 4289.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.146990 restraints weight = 2595.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.149712 restraints weight = 1864.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.151663 restraints weight = 1480.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.152744 restraints weight = 1251.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3502  Z= 0.158
  Angle     :  0.584   8.214   4762  Z= 0.293
  Chirality :  0.042   0.146    505
  Planarity :  0.005   0.085    620
  Dihedral  :  4.762  22.182    505
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 15.26 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.41), residues: 431
  helix: -1.42 (0.98), residues: 28
  sheet:  0.20 (0.47), residues: 131
  loop : -0.47 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 457 
 TYR   0.016   0.001   TYR L  91 
 PHE   0.012   0.001   PHE H  27 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 3496)
  covalent geometry    : angle       0.58191 ( 4749)
  SS BOND              : bond        0.00288 (    5)
  SS BOND              : angle       1.11364 (   10)
  hydrogen bonds       : bond        0.03140 (  102)
  hydrogen bonds       : angle       6.70704 (  255)
  link_NAG-ASN         : bond        0.00211 (    1)
  link_NAG-ASN         : angle       1.11597 (    3)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7938 (m-80) cc_final: 0.7699 (m-80)
REVERT: A  468 ILE cc_start: 0.9133 (pt) cc_final: 0.8757 (mt)
REVERT: L   87 TYR cc_start: 0.7993 (m-80) cc_final: 0.7760 (m-80)
  outliers start: 16
  outliers final: 12
  residues processed: 91
  average time/residue: 0.0941
  time to fit residues: 9.9520
Evaluate side-chains
  89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   56 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  102 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0670
   chunk 5 optimal weight:    0.0980
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
** L  38 GLN ** 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 = 0.3930 r_free = 0.3930 target = 0.159330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.134256 restraints weight = 4304.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.138192 restraints weight = 2636.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.140787 restraints weight = 1909.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.142328 restraints weight = 1521.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.143619 restraints weight = 1307.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3502  Z= 0.132
  Angle     :  0.586   8.913   4762  Z= 0.285
  Chirality :  0.042   0.143    505
  Planarity :  0.005   0.090    620
  Dihedral  :  4.661  24.190    505
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.44 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.41), residues: 431
  helix: -1.31 (1.01), residues: 28
  sheet:  0.49 (0.48), residues: 127
  loop : -0.56 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 457 
 TYR   0.010   0.001   TYR L  91 
 PHE   0.010   0.001   PHE H  27 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3496)
  covalent geometry    : angle       0.58434 ( 4749)
  SS BOND              : bond        0.00265 (    5)
  SS BOND              : angle       0.91111 (   10)
  hydrogen bonds       : bond        0.02879 (  102)
  hydrogen bonds       : angle       6.43141 (  255)
  link_NAG-ASN         : bond        0.00213 (    1)
  link_NAG-ASN         : angle       1.01865 (    3)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7902 (m-80) cc_final: 0.7625 (m-80)
REVERT: A  468 ILE cc_start: 0.9124 (pt) cc_final: 0.8782 (mt)
  outliers start: 13
  outliers final: 11
  residues processed: 87
  average time/residue: 0.0844
  time to fit residues: 8.7042
Evaluate side-chains
  87 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  100 TYR
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 23 optimal weight:    0.0050
   chunk 32 optimal weight:    0.0030
   chunk 30 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   chunk 35 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.3004

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

Flipped N/Q/H residues before XYZ refinement:
H  76 ASN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.163603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.137861 restraints weight = 4486.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.141786 restraints weight = 2718.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.144431 restraints weight = 1963.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.146190 restraints weight = 1569.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.147267 restraints weight = 1333.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3502  Z= 0.110
  Angle     :  0.551   8.675   4762  Z= 0.270
  Chirality :  0.041   0.137    505
  Planarity :  0.005   0.088    620
  Dihedral  :  4.456  23.195    505
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 21.25 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.42), residues: 431
  helix: -1.26 (1.02), residues: 28
  sheet:  0.32 (0.47), residues: 133
  loop : -0.47 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 100J
 TYR   0.008   0.001   TYR A 495 
 PHE   0.010   0.001   PHE H  27 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 3496)
  covalent geometry    : angle       0.54954 ( 4749)
  SS BOND              : bond        0.00224 (    5)
  SS BOND              : angle       0.81545 (   10)
  hydrogen bonds       : bond        0.02704 (  102)
  hydrogen bonds       : angle       6.22606 (  255)
  link_NAG-ASN         : bond        0.00220 (    1)
  link_NAG-ASN         : angle       0.92658 (    3)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  468 ILE cc_start: 0.9135 (pt) cc_final: 0.8796 (mt)
  outliers start: 10
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0909
  time to fit residues: 9.0006
Evaluate side-chains
  81 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  100 TYR
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    0.1980
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0030
   chunk 12 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0000
   chunk 9 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 7 optimal weight:    0.2980
   overall best weight:    0.2194

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  64 GLN
H  76 ASN
L  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.164964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.139586 restraints weight = 4397.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.143379 restraints weight = 2693.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.146019 restraints weight = 1953.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.147504 restraints weight = 1557.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.148812 restraints weight = 1344.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   3502  Z= 0.100
  Angle     :  0.578   9.161   4762  Z= 0.276
  Chirality :  0.041   0.134    505
  Planarity :  0.005   0.089    620
  Dihedral  :  4.307  23.241    505
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 22.89 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.42), residues: 431
  helix: -1.25 (1.04), residues: 28
  sheet:  0.44 (0.47), residues: 133
  loop : -0.45 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 100J
 TYR   0.007   0.001   TYR A 453 
 PHE   0.008   0.001   PHE H  27 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 3496)
  covalent geometry    : angle       0.57730 ( 4749)
  SS BOND              : bond        0.00201 (    5)
  SS BOND              : angle       0.67766 (   10)
  hydrogen bonds       : bond        0.02578 (  102)
  hydrogen bonds       : angle       6.05577 (  255)
  link_NAG-ASN         : bond        0.00232 (    1)
  link_NAG-ASN         : angle       0.85754 (    3)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  468 ILE cc_start: 0.9113 (pt) cc_final: 0.8815 (mt)
REVERT: H   34 MET cc_start: 0.8063 (mmm) cc_final: 0.7845 (mmm)
  outliers start: 9
  outliers final: 7
  residues processed: 79
  average time/residue: 0.0817
  time to fit residues: 7.7025
Evaluate side-chains
  80 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  100 TYR
Chi-restraints excluded: chain L residue   38 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 31 optimal weight:    0.2980
   chunk 17 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0040
   chunk 23 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0770
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.2950

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** 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 = 0.3966 r_free = 0.3966 target = 0.162267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.137200 restraints weight = 4395.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.141163 restraints weight = 2662.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.143803 restraints weight = 1912.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.145375 restraints weight = 1519.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.146763 restraints weight = 1302.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3502  Z= 0.111
  Angle     :  0.569   8.506   4762  Z= 0.277
  Chirality :  0.042   0.136    505
  Planarity :  0.005   0.090    620
  Dihedral  :  4.319  22.868    505
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 22.07 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.42), residues: 431
  helix: -1.20 (1.06), residues: 28
  sheet:  0.59 (0.48), residues: 131
  loop : -0.38 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  61 
 TYR   0.008   0.001   TYR A 453 
 PHE   0.008   0.001   PHE H  27 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3496)
  covalent geometry    : angle       0.56861 ( 4749)
  SS BOND              : bond        0.00229 (    5)
  SS BOND              : angle       0.70092 (   10)
  hydrogen bonds       : bond        0.02592 (  102)
  hydrogen bonds       : angle       6.00416 (  255)
  link_NAG-ASN         : bond        0.00208 (    1)
  link_NAG-ASN         : angle       0.95184 (    3)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  468 ILE cc_start: 0.9123 (pt) cc_final: 0.8819 (mt)
REVERT: H   34 MET cc_start: 0.8051 (mmm) cc_final: 0.7848 (mmm)
  outliers start: 10
  outliers final: 8
  residues processed: 84
  average time/residue: 0.0756
  time to fit residues: 7.5007
Evaluate side-chains
  80 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  100 TYR
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:    0.5980
   chunk 19 optimal weight:    0.1980
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.159536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.134326 restraints weight = 4404.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.138103 restraints weight = 2663.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.140602 restraints weight = 1928.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.142152 restraints weight = 1551.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.143472 restraints weight = 1338.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3502  Z= 0.148
  Angle     :  0.616   9.545   4762  Z= 0.296
  Chirality :  0.042   0.145    505
  Planarity :  0.006   0.092    620
  Dihedral  :  4.531  23.168    505
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 22.07 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.42), residues: 431
  helix: -1.14 (1.07), residues: 28
  sheet:  0.38 (0.48), residues: 135
  loop : -0.41 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 100J
 TYR   0.009   0.001   TYR L  91 
 PHE   0.009   0.001   PHE H  27 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.006   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 3496)
  covalent geometry    : angle       0.61528 ( 4749)
  SS BOND              : bond        0.00293 (    5)
  SS BOND              : angle       0.84837 (   10)
  hydrogen bonds       : bond        0.02751 (  102)
  hydrogen bonds       : angle       6.13747 (  255)
  link_NAG-ASN         : bond        0.00173 (    1)
  link_NAG-ASN         : angle       1.22489 (    3)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  468 ILE cc_start: 0.9133 (pt) cc_final: 0.8772 (mt)
  outliers start: 14
  outliers final: 10
  residues processed: 85
  average time/residue: 0.0802
  time to fit residues: 8.1610
Evaluate side-chains
  80 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    0.0050
   chunk 1 optimal weight:    0.0770
   chunk 9 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 7 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.3152

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  64 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.161402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.136346 restraints weight = 4279.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.140211 restraints weight = 2607.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.142743 restraints weight = 1882.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.144268 restraints weight = 1511.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.145580 restraints weight = 1303.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3502  Z= 0.116
  Angle     :  0.578   8.911   4762  Z= 0.283
  Chirality :  0.042   0.136    505
  Planarity :  0.005   0.090    620
  Dihedral  :  4.445  23.236    505
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 22.34 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.42), residues: 431
  helix: -1.19 (1.07), residues: 28
  sheet:  0.81 (0.48), residues: 127
  loop : -0.46 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 100J
 TYR   0.008   0.001   TYR A 453 
 PHE   0.009   0.001   PHE H  27 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.006   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3496)
  covalent geometry    : angle       0.57696 ( 4749)
  SS BOND              : bond        0.00258 (    5)
  SS BOND              : angle       0.73488 (   10)
  hydrogen bonds       : bond        0.02602 (  102)
  hydrogen bonds       : angle       6.03266 (  255)
  link_NAG-ASN         : bond        0.00221 (    1)
  link_NAG-ASN         : angle       1.00208 (    3)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  468 ILE cc_start: 0.9141 (pt) cc_final: 0.8837 (mt)
  outliers start: 9
  outliers final: 9
  residues processed: 79
  average time/residue: 0.0784
  time to fit residues: 7.4430
Evaluate side-chains
  81 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.0040
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0470
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0370
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.2968

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** 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 = 0.3972 r_free = 0.3972 target = 0.163632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.137716 restraints weight = 4378.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.141744 restraints weight = 2678.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.144351 restraints weight = 1942.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.145934 restraints weight = 1561.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.147368 restraints weight = 1345.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3502  Z= 0.113
  Angle     :  0.586   8.816   4762  Z= 0.286
  Chirality :  0.042   0.135    505
  Planarity :  0.005   0.091    620
  Dihedral  :  4.371  23.175    505
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 23.43 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.42), residues: 431
  helix: -1.11 (1.08), residues: 28
  sheet:  0.86 (0.48), residues: 127
  loop : -0.46 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 100J
 TYR   0.007   0.001   TYR A 453 
 PHE   0.009   0.001   PHE H  27 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.006   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3496)
  covalent geometry    : angle       0.58563 ( 4749)
  SS BOND              : bond        0.00244 (    5)
  SS BOND              : angle       0.69700 (   10)
  hydrogen bonds       : bond        0.02536 (  102)
  hydrogen bonds       : angle       5.96748 (  255)
  link_NAG-ASN         : bond        0.00219 (    1)
  link_NAG-ASN         : angle       1.04687 (    3)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  468 ILE cc_start: 0.9154 (pt) cc_final: 0.8861 (mt)
  outliers start: 8
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0657
  time to fit residues: 6.3486
Evaluate side-chains
  84 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 41 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  64 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.160475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.134322 restraints weight = 4431.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.138250 restraints weight = 2713.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.140602 restraints weight = 1984.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.142536 restraints weight = 1610.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.143618 restraints weight = 1382.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3502  Z= 0.172
  Angle     :  0.619   9.452   4762  Z= 0.306
  Chirality :  0.042   0.144    505
  Planarity :  0.006   0.093    620
  Dihedral  :  4.734  23.432    505
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 22.62 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.42), residues: 431
  helix: -1.15 (1.06), residues: 28
  sheet:  0.43 (0.49), residues: 125
  loop : -0.46 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 100J
 TYR   0.009   0.001   TYR A 495 
 PHE   0.009   0.001   PHE H  27 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.007   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 3496)
  covalent geometry    : angle       0.61706 ( 4749)
  SS BOND              : bond        0.00351 (    5)
  SS BOND              : angle       0.89657 (   10)
  hydrogen bonds       : bond        0.02826 (  102)
  hydrogen bonds       : angle       6.20869 (  255)
  link_NAG-ASN         : bond        0.00197 (    1)
  link_NAG-ASN         : angle       1.39590 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 913.88 seconds
wall clock time: 16 minutes 24.77 seconds (984.77 seconds total)