Starting phenix.real_space_refine
on Wed Jul  1 22:13:38 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7won_32652/07_2026/7won_32652.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7won_32652/07_2026/7won_32652.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7won_32652/07_2026/7won_32652.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7won_32652/07_2026/7won_32652.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7won_32652/07_2026/7won_32652.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7won_32652/07_2026/7won_32652.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7won_32652/07_2026/7won_32652.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7won_32652/07_2026/7won_32652.cif"
  }
  resolution = 3.9
  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=   0.010
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      15      5.16       5
     C    2098      2.51       5
     N     556      2.21       5
     O     649      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3318
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "F"
      Number of atoms: 1462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1462
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 9, 'TRANS': 173}
    Chain: "L"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 811
          Classifications: {'peptide': 111}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 1017
          Classifications: {'peptide': 131}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 128}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 0.68, per 1000 atoms: 0.20
  Number of scatterers: 3318
  At special positions: 0
  Unit cell: (73.132, 84.024, 80.912, 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      15     16.00
     O     649      8.00
     N     556      7.00
     C    2098      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS F 379 " - pdb=" SG  CYS F 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN F 343 "
  Time building additional restraints: 0.17
  Conformation dependent library (CDL) restraints added in 102.6 milliseconds
  

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  760

  Finding SS restraints...
    Secondary structure from input PDB file:
      1 helices and 8 sheets defined
      1.4% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'F' and resid 405 through 410
      removed outlier: 4.532A  pdb=" N   ARG F 408 " --> pdb=" O   ASP F 405 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 356 through 358
      removed outlier: 3.564A  pdb=" N   LYS F 356 " --> pdb=" O   ALA F 397 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   CYS F 432 " --> pdb=" O   LEU F 513 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'L' and resid 17 through 23
      removed outlier: 3.501A  pdb=" N   SER L  69 " --> pdb=" O   SER L  72 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   SER L  74 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 47 through 51
      removed outlier: 5.896A  pdb=" N   LEU L  48 " --> pdb=" O   GLN L  39 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   GLN L  39 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7
      removed outlier: 3.748A  pdb=" N   SER H   7 " --> pdb=" O   SER H  21 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   LEU H  18 " --> pdb=" O   MET H  83 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   MET H  83 " --> pdb=" O   LEU H  18 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.113A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 102 through 104

    66 hydrogen bonds defined for protein.
    168 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: 0.25

  Time building geometry restraints manager: 0.22 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 538
        1.30 -     1.43: 1004
        1.43 -     1.56: 1840
        1.56 -     1.69: 0
        1.69 -     1.82: 19
  Bond restraints: 3401
  Sorted by residual:
  bond pdb=" C   ARG H 106 "
       pdb=" N   SER H 107 "
    ideal  model  delta    sigma   weight residual
    1.332  1.240  0.092 1.40e-02 5.10e+03 4.33e+01
  bond pdb=" C   ARG H 106 "
       pdb=" O   ARG H 106 "
    ideal  model  delta    sigma   weight residual
    1.237  1.171  0.066 1.16e-02 7.43e+03 3.19e+01
  bond pdb=" CA  ASP H 113 "
       pdb=" C   ASP H 113 "
    ideal  model  delta    sigma   weight residual
    1.523  1.453  0.070 1.28e-02 6.10e+03 2.98e+01
  bond pdb=" CA  ARG H 106 "
       pdb=" C   ARG H 106 "
    ideal  model  delta    sigma   weight residual
    1.524  1.477  0.046 1.26e-02 6.30e+03 1.35e+01
  bond pdb=" CA  ARG H 106 "
       pdb=" CB  ARG H 106 "
    ideal  model  delta    sigma   weight residual
    1.529  1.473  0.056 1.58e-02 4.01e+03 1.27e+01
  ... (remaining 3396 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.84: 4523
        2.84 -     5.69: 80
        5.69 -     8.53: 12
        8.53 -    11.37: 2
       11.37 -    14.22: 3
  Bond angle restraints: 4620
  Sorted by residual:
  angle pdb=" N   TYR H 103 "
        pdb=" CA  TYR H 103 "
        pdb=" C   TYR H 103 "
      ideal   model   delta    sigma   weight residual
     109.52  121.19  -11.67 1.55e+00 4.16e-01 5.67e+01
  angle pdb=" O   VAL H 100 "
        pdb=" C   VAL H 100 "
        pdb=" N   GLN H 101 "
      ideal   model   delta    sigma   weight residual
     122.57  114.38    8.19 1.25e+00 6.40e-01 4.30e+01
  angle pdb=" N   LEU H 112 "
        pdb=" CA  LEU H 112 "
        pdb=" C   LEU H 112 "
      ideal   model   delta    sigma   weight residual
     110.35  101.53    8.82 1.36e+00 5.41e-01 4.21e+01
  angle pdb=" C   ARG H 106 "
        pdb=" N   SER H 107 "
        pdb=" CA  SER H 107 "
      ideal   model   delta    sigma   weight residual
     121.54  109.28   12.26 1.91e+00 2.74e-01 4.12e+01
  angle pdb=" CA  ARG H 106 "
        pdb=" C   ARG H 106 "
        pdb=" O   ARG H 106 "
      ideal   model   delta    sigma   weight residual
     120.70  127.27   -6.57 1.03e+00 9.43e-01 4.06e+01
  ... (remaining 4615 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 1740
       17.23 -    34.46: 175
       34.46 -    51.69: 33
       51.69 -    68.92: 7
       68.92 -    86.14: 4
  Dihedral angle restraints: 1959
    sinusoidal: 745
      harmonic: 1214
  Sorted by residual:
  dihedral pdb=" CA  PHE F 429 "
           pdb=" C   PHE F 429 "
           pdb=" N   THR F 430 "
           pdb=" CA  THR F 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.21   28.79     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  ASN F 460 "
           pdb=" C   ASN F 460 "
           pdb=" N   LEU F 461 "
           pdb=" CA  LEU F 461 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.65  -25.35     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  CYS F 336 "
           pdb=" C   CYS F 336 "
           pdb=" N   PRO F 337 "
           pdb=" CA  PRO F 337 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.93  -19.07     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 1956 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 365
       0.059 -    0.119: 101
       0.119 -    0.178: 19
       0.178 -    0.238: 6
       0.238 -    0.297: 1
  Chirality restraints: 492
  Sorted by residual:
  chirality pdb=" CA  ASP H 113 "
            pdb=" N   ASP H 113 "
            pdb=" C   ASP H 113 "
            pdb=" CB  ASP H 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  TYR H 103 "
            pdb=" N   TYR H 103 "
            pdb=" C   TYR H 103 "
            pdb=" CB  TYR H 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN F 343 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 489 not shown)

  Planarity restraints: 601
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL H 100 "    0.042 2.00e-02 2.50e+03   7.95e-02 6.33e+01
        pdb=" C   VAL H 100 "   -0.138 2.00e-02 2.50e+03
        pdb=" O   VAL H 100 "    0.051 2.00e-02 2.50e+03
        pdb=" N   GLN H 101 "    0.045 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 462 "    0.042 5.00e-02 4.00e+02   6.32e-02 6.39e+00
        pdb=" N   PRO F 463 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO F 463 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO F 463 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG L  56 "    0.040 5.00e-02 4.00e+02   6.06e-02 5.87e+00
        pdb=" N   PRO L  57 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO L  57 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO L  57 "    0.033 5.00e-02 4.00e+02
  ... (remaining 598 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 50
        2.61 -     3.18: 2613
        3.18 -     3.75: 4748
        3.75 -     4.33: 6402
        4.33 -     4.90: 10870
  Nonbonded interactions: 24683
  Sorted by model distance:
  nonbonded pdb=" O   ARG H 106 "
            pdb=" C   SER H 107 "
     model   vdw
     2.035 3.270
  nonbonded pdb=" O   SER F 371 "
            pdb=" NH1 ARG H 106 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" O   ASN F 439 "
            pdb=" OG  SER F 443 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   ARG H 106 "
            pdb=" CA  SER H 107 "
     model   vdw
     2.278 2.776
  nonbonded pdb=" OG  SER F 349 "
            pdb=" O   LEU F 452 "
     model   vdw
     2.302 3.040
  ... (remaining 24678 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=0.00 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:             14.620
  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:                    0.000
  Process input model:                     3.290
  Find NCS groups from input model:        0.010
  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:0.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.092   3406  Z= 0.359
  Angle     :  0.978  14.217   4632  Z= 0.563
  Chirality :  0.060   0.297    492
  Planarity :  0.008   0.080    600
  Dihedral  : 14.560  86.144   1190
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.79 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 10.14 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.42 (0.35), residues: 419
  helix: -4.82 (0.44), residues: 14
  sheet: -2.40 (0.44), residues: 127
  loop : -3.30 (0.30), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 106 
 TYR   0.021   0.002   TYR H 104 
 PHE   0.011   0.002   PHE F 400 
 TRP   0.033   0.002   TRP F 436 
 HIS   0.006   0.003   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00604 /  0.36 ( 3401)
  covalent geometry    : angle       0.97704 /  0.56 ( 4620)
  SS BOND              : bond        0.00241 /  0.13 (    3)
  SS BOND              : angle       0.61938 /  0.35 (    6)
  hydrogen bonds       : bond        0.30355 / 17.66 (   66)
  hydrogen bonds       : angle      11.76116 /  8.23 (  168)
  link_BETA1-4         : bond        0.01260 /  0.66 (    1)
  link_BETA1-4         : angle       2.10600 /  1.11 (    3)
  link_NAG-ASN         : bond        0.00107 /  0.06 (    1)
  link_NAG-ASN         : angle       0.76846 /  0.40 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: F  354 ASN cc_start: 0.8755 (p0) cc_final: 0.8455 (p0)
REVERT: F  474 GLN cc_start: 0.6126 (tp40) cc_final: 0.5871 (tm-30)
REVERT: L   16 GLN cc_start: 0.8731 (mm110) cc_final: 0.8169 (mp10)
REVERT: H   16 ARG cc_start: 0.2340 (mmt180) cc_final: 0.1973 (mmt180)
  outliers start: 1
  outliers final: 1
  residues processed: 95
  average time/residue: 0.0610
  time to fit residues: 6.9206
Evaluate side-chains
  77 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  106 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.1980
   chunk 22 optimal weight:    0.0770
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.6140

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 370 ASN
F 388 ASN
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 414 GLN
F 487 ASN
L   6 GLN
L  16 GLN
L  40 GLN
H  13 GLN
H  39 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.139581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.112038 restraints weight = 5054.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.115736 restraints weight = 3212.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.118278 restraints weight = 2380.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.120032 restraints weight = 1940.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.120938 restraints weight = 1685.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3276
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (13 function evaluations)
r_final: 0.3275
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3406  Z= 0.184
  Angle     :  0.653   8.252   4632  Z= 0.336
  Chirality :  0.046   0.167    492
  Planarity :  0.005   0.043    600
  Dihedral  :  6.109  55.091    480
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.22 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 18.31 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.97 (0.38), residues: 419
  helix: -4.56 (0.72), residues: 14
  sheet: -2.28 (0.44), residues: 132
  loop : -2.85 (0.34), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H  72 
 TYR   0.014   0.002   TYR F 495 
 PHE   0.015   0.002   PHE F 338 
 TRP   0.017   0.001   TRP F 436 
 HIS   0.003   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.18 ( 3401)
  covalent geometry    : angle       0.65279 /  0.34 ( 4620)
  SS BOND              : bond        0.00236 /  0.12 (    3)
  SS BOND              : angle       0.60930 /  0.35 (    6)
  hydrogen bonds       : bond        0.05494 /  3.39 (   66)
  hydrogen bonds       : angle       8.08313 /  5.46 (  168)
  link_BETA1-4         : bond        0.00781 /  0.41 (    1)
  link_BETA1-4         : angle       0.92646 /  0.45 (    3)
  link_NAG-ASN         : bond        0.00089 /  0.05 (    1)
  link_NAG-ASN         : angle       0.64449 /  0.35 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.074 
Fit side-chains
REVERT: F  354 ASN cc_start: 0.8903 (p0) cc_final: 0.8587 (p0)
REVERT: F  474 GLN cc_start: 0.6106 (tp40) cc_final: 0.5788 (tm-30)
REVERT: L    6 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8755 (pt0)
REVERT: L   16 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8036 (mp10)
REVERT: H   16 ARG cc_start: 0.2102 (mmt180) cc_final: 0.1793 (mmt180)
  outliers start: 15
  outliers final: 9
  residues processed: 94
  average time/residue: 0.0632
  time to fit residues: 6.9179
Evaluate side-chains
  88 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  402 ILE
Chi-restraints excluded: chain F residue  427 ASP
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   35 VAL
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain H residue  126 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0670
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 22 optimal weight:    0.2980
   chunk 26 optimal weight:    0.0570
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.3436

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   6 GLN
L  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.138751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.117775 restraints weight = 4990.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.120373 restraints weight = 3290.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.122342 restraints weight = 2497.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.123781 restraints weight = 2062.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.124497 restraints weight = 1783.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3406  Z= 0.126
  Angle     :  0.609   9.392   4632  Z= 0.307
  Chirality :  0.045   0.177    492
  Planarity :  0.004   0.037    600
  Dihedral  :  5.089  21.928    476
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.56 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.57 (0.39), residues: 419
  helix: -4.52 (0.77), residues: 14
  sheet: -1.99 (0.45), residues: 133
  loop : -2.57 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  19 
 TYR   0.013   0.001   TYR F 369 
 PHE   0.009   0.001   PHE F 338 
 TRP   0.012   0.001   TRP F 436 
 HIS   0.003   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 3401)
  covalent geometry    : angle       0.60861 /  0.31 ( 4620)
  SS BOND              : bond        0.00220 /  0.11 (    3)
  SS BOND              : angle       0.62293 /  0.34 (    6)
  hydrogen bonds       : bond        0.04290 /  2.58 (   66)
  hydrogen bonds       : angle       7.19400 /  4.82 (  168)
  link_BETA1-4         : bond        0.00699 /  0.37 (    1)
  link_BETA1-4         : angle       0.98244 /  0.48 (    3)
  link_NAG-ASN         : bond        0.00071 /  0.04 (    1)
  link_NAG-ASN         : angle       0.56548 /  0.31 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
REVERT: F  354 ASN cc_start: 0.8826 (p0) cc_final: 0.8510 (p0)
REVERT: F  474 GLN cc_start: 0.5882 (tp40) cc_final: 0.5349 (tm-30)
REVERT: L   16 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8101 (mp10)
REVERT: H   16 ARG cc_start: 0.2422 (mmt180) cc_final: 0.0288 (mmt180)
REVERT: H   25 SER cc_start: 0.9347 (t) cc_final: 0.9020 (m)
REVERT: H  113 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8552 (m-30)
REVERT: H  114 TYR cc_start: 0.7595 (m-80) cc_final: 0.7385 (m-80)
  outliers start: 13
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0684
  time to fit residues: 7.1650
Evaluate side-chains
  90 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  402 ILE
Chi-restraints excluded: chain F residue  433 VAL
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain H residue  113 ASP
Chi-restraints excluded: chain H residue  126 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 2 optimal weight:    0.2980
   chunk 12 optimal weight:    0.3980
   chunk 39 optimal weight:    0.0030
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.3790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 409 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 = 0.3544 r_free = 0.3544 target = 0.138946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.117003 restraints weight = 4985.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.120131 restraints weight = 3145.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.122265 restraints weight = 2301.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.123437 restraints weight = 1852.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.124505 restraints weight = 1615.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3406  Z= 0.132
  Angle     :  0.602   9.379   4632  Z= 0.302
  Chirality :  0.045   0.188    492
  Planarity :  0.004   0.032    600
  Dihedral  :  4.926  22.611    476
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.02 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.00 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.38 (0.40), residues: 419
  helix: -4.54 (0.75), residues: 14
  sheet: -1.83 (0.46), residues: 133
  loop : -2.44 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 346 
 TYR   0.012   0.001   TYR F 369 
 PHE   0.010   0.001   PHE F 338 
 TRP   0.011   0.001   TRP F 436 
 HIS   0.004   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 3401)
  covalent geometry    : angle       0.60190 /  0.30 ( 4620)
  SS BOND              : bond        0.00289 /  0.14 (    3)
  SS BOND              : angle       0.70398 /  0.38 (    6)
  hydrogen bonds       : bond        0.03996 /  2.38 (   66)
  hydrogen bonds       : angle       6.76585 /  4.48 (  168)
  link_BETA1-4         : bond        0.00556 /  0.29 (    1)
  link_BETA1-4         : angle       0.95327 /  0.46 (    3)
  link_NAG-ASN         : bond        0.00005 /  0.00 (    1)
  link_NAG-ASN         : angle       0.60799 /  0.33 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.084 
Fit side-chains
REVERT: F  354 ASN cc_start: 0.8850 (p0) cc_final: 0.8518 (p0)
REVERT: F  474 GLN cc_start: 0.5932 (tp40) cc_final: 0.5377 (tm-30)
REVERT: L   16 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8099 (mp10)
REVERT: H   16 ARG cc_start: 0.2443 (mmt180) cc_final: -0.0574 (mpt180)
REVERT: H   25 SER cc_start: 0.9330 (t) cc_final: 0.9019 (m)
REVERT: H  113 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8530 (m-30)
REVERT: H  114 TYR cc_start: 0.7718 (m-80) cc_final: 0.7471 (m-80)
  outliers start: 13
  outliers final: 9
  residues processed: 86
  average time/residue: 0.0580
  time to fit residues: 6.0220
Evaluate side-chains
  85 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  402 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   35 VAL
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue   72 SER
Chi-restraints excluded: chain H residue  113 ASP
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain H residue  126 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 32 optimal weight:    0.1980
   chunk 5 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 409 GLN
F 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.136229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.114460 restraints weight = 5020.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.117129 restraints weight = 3341.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.119050 restraints weight = 2569.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.120231 restraints weight = 2129.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.120986 restraints weight = 1874.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3406  Z= 0.175
  Angle     :  0.640   8.988   4632  Z= 0.319
  Chirality :  0.046   0.161    492
  Planarity :  0.004   0.032    600
  Dihedral  :  5.061  22.663    476
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.22 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 21.13 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.27 (0.40), residues: 419
  helix: -4.61 (0.68), residues: 14
  sheet: -1.80 (0.46), residues: 133
  loop : -2.33 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 346 
 TYR   0.013   0.001   TYR F 495 
 PHE   0.014   0.002   PHE F 338 
 TRP   0.016   0.002   TRP F 436 
 HIS   0.005   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00409 /  0.17 ( 3401)
  covalent geometry    : angle       0.63914 /  0.32 ( 4620)
  SS BOND              : bond        0.00217 /  0.11 (    3)
  SS BOND              : angle       0.72607 /  0.41 (    6)
  hydrogen bonds       : bond        0.04126 /  2.49 (   66)
  hydrogen bonds       : angle       6.57277 /  4.32 (  168)
  link_BETA1-4         : bond        0.00659 /  0.35 (    1)
  link_BETA1-4         : angle       1.10334 /  0.54 (    3)
  link_NAG-ASN         : bond        0.00168 /  0.09 (    1)
  link_NAG-ASN         : angle       0.79959 /  0.45 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.085 
Fit side-chains
REVERT: F  354 ASN cc_start: 0.8854 (p0) cc_final: 0.8537 (p0)
REVERT: F  474 GLN cc_start: 0.5970 (tp40) cc_final: 0.5407 (tm-30)
REVERT: L   16 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8132 (mp10)
REVERT: H   16 ARG cc_start: 0.2414 (mmt180) cc_final: 0.0191 (mmt180)
REVERT: H  114 TYR cc_start: 0.7793 (m-80) cc_final: 0.7550 (m-80)
  outliers start: 19
  outliers final: 13
  residues processed: 88
  average time/residue: 0.0545
  time to fit residues: 5.7462
Evaluate side-chains
  89 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   35 VAL
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue   72 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain H residue  127 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.0570
   chunk 15 optimal weight:    0.0970
   chunk 1 optimal weight:    0.6980
   chunk 35 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0030
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.2506

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.139225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.117169 restraints weight = 4992.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.120105 restraints weight = 3269.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.122085 restraints weight = 2460.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.123368 restraints weight = 2028.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.124458 restraints weight = 1770.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3406  Z= 0.111
  Angle     :  0.595   9.005   4632  Z= 0.292
  Chirality :  0.044   0.147    492
  Planarity :  0.004   0.032    600
  Dihedral  :  4.647  20.669    476
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 23.10 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.00 (0.41), residues: 419
  helix: -4.51 (0.79), residues: 14
  sheet: -1.53 (0.47), residues: 134
  loop : -2.19 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  72 
 TYR   0.010   0.001   TYR F 369 
 PHE   0.010   0.001   PHE F 456 
 TRP   0.008   0.001   TRP F 436 
 HIS   0.005   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.11 ( 3401)
  covalent geometry    : angle       0.59388 /  0.29 ( 4620)
  SS BOND              : bond        0.00260 /  0.13 (    3)
  SS BOND              : angle       0.76058 /  0.43 (    6)
  hydrogen bonds       : bond        0.03240 /  1.92 (   66)
  hydrogen bonds       : angle       6.21730 /  4.17 (  168)
  link_BETA1-4         : bond        0.00799 /  0.42 (    1)
  link_BETA1-4         : angle       1.07463 /  0.53 (    3)
  link_NAG-ASN         : bond        0.00045 /  0.02 (    1)
  link_NAG-ASN         : angle       0.59139 /  0.32 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.112 
Fit side-chains
REVERT: F  354 ASN cc_start: 0.8801 (p0) cc_final: 0.8461 (p0)
REVERT: F  474 GLN cc_start: 0.5796 (tp40) cc_final: 0.5325 (tm-30)
REVERT: L   16 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8082 (mp10)
REVERT: H   16 ARG cc_start: 0.2482 (mmt180) cc_final: -0.0455 (mpt180)
REVERT: H   25 SER cc_start: 0.9297 (t) cc_final: 0.9025 (m)
REVERT: H   53 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.7238 (t80)
REVERT: H  113 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8502 (m-30)
  outliers start: 13
  outliers final: 11
  residues processed: 95
  average time/residue: 0.0590
  time to fit residues: 6.7725
Evaluate side-chains
  91 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   35 VAL
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue   72 SER
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  113 ASP
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain H residue  126 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0050
   chunk 30 optimal weight:    0.1980
   chunk 21 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0770
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.3552

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.137351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.115581 restraints weight = 5004.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.118350 restraints weight = 3286.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.120154 restraints weight = 2468.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.121633 restraints weight = 2034.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.122564 restraints weight = 1769.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3406  Z= 0.128
  Angle     :  0.615   8.906   4632  Z= 0.303
  Chirality :  0.045   0.148    492
  Planarity :  0.004   0.031    600
  Dihedral  :  4.701  20.641    476
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 23.66 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.99 (0.40), residues: 419
  helix: -4.93 (0.43), residues: 20
  sheet: -1.48 (0.47), residues: 128
  loop : -2.09 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  72 
 TYR   0.028   0.001   TYR H 114 
 PHE   0.010   0.001   PHE F 429 
 TRP   0.011   0.001   TRP F 436 
 HIS   0.005   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 3401)
  covalent geometry    : angle       0.61451 /  0.30 ( 4620)
  SS BOND              : bond        0.00217 /  0.11 (    3)
  SS BOND              : angle       0.75198 /  0.42 (    6)
  hydrogen bonds       : bond        0.03342 /  2.02 (   66)
  hydrogen bonds       : angle       6.07395 /  4.09 (  168)
  link_BETA1-4         : bond        0.00759 /  0.40 (    1)
  link_BETA1-4         : angle       1.06770 /  0.52 (    3)
  link_NAG-ASN         : bond        0.00027 /  0.01 (    1)
  link_NAG-ASN         : angle       0.64433 /  0.36 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.074 
Fit side-chains
REVERT: F  354 ASN cc_start: 0.8826 (p0) cc_final: 0.8491 (p0)
REVERT: F  474 GLN cc_start: 0.5857 (tp40) cc_final: 0.5351 (tm-30)
REVERT: L   16 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8088 (mp10)
REVERT: H   16 ARG cc_start: 0.2432 (mmt180) cc_final: -0.0535 (mpt180)
REVERT: H   25 SER cc_start: 0.9319 (t) cc_final: 0.9052 (m)
REVERT: H  113 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8419 (m-30)
  outliers start: 13
  outliers final: 12
  residues processed: 88
  average time/residue: 0.0646
  time to fit residues: 6.7584
Evaluate side-chains
  91 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  452 LEU
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   35 VAL
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue   63 ARG
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  113 ASP
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain H residue  126 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 5 optimal weight:    0.2980
   chunk 22 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  40 GLN
H  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.133067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.112321 restraints weight = 5096.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.114649 restraints weight = 3543.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.116315 restraints weight = 2783.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.117556 restraints weight = 2347.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.117569 restraints weight = 2074.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3406  Z= 0.178
  Angle     :  0.662   8.952   4632  Z= 0.327
  Chirality :  0.046   0.200    492
  Planarity :  0.004   0.030    600
  Dihedral  :  4.996  21.815    476
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.79 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 23.10 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.40), residues: 419
  helix: -4.91 (0.45), residues: 20
  sheet: -1.55 (0.48), residues: 127
  loop : -2.10 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  72 
 TYR   0.031   0.002   TYR H 114 
 PHE   0.013   0.002   PHE F 338 
 TRP   0.017   0.002   TRP F 436 
 HIS   0.005   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00415 /  0.18 ( 3401)
  covalent geometry    : angle       0.65651 /  0.32 ( 4620)
  SS BOND              : bond        0.00163 /  0.08 (    3)
  SS BOND              : angle       2.42098 /  1.44 (    6)
  hydrogen bonds       : bond        0.03661 /  2.19 (   66)
  hydrogen bonds       : angle       5.99908 /  4.02 (  168)
  link_BETA1-4         : bond        0.00776 /  0.41 (    1)
  link_BETA1-4         : angle       1.08021 /  0.53 (    3)
  link_NAG-ASN         : bond        0.00149 /  0.08 (    1)
  link_NAG-ASN         : angle       0.86025 /  0.50 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.075 
Fit side-chains
REVERT: F  354 ASN cc_start: 0.8824 (p0) cc_final: 0.8466 (p0)
REVERT: F  474 GLN cc_start: 0.5899 (tp40) cc_final: 0.5378 (tm-30)
REVERT: L   16 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8092 (mp10)
REVERT: H   16 ARG cc_start: 0.2446 (mmt180) cc_final: 0.0197 (mmt180)
REVERT: H   96 CYS cc_start: 0.6598 (p) cc_final: 0.6003 (p)
REVERT: H  113 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8326 (m-30)
  outliers start: 15
  outliers final: 14
  residues processed: 85
  average time/residue: 0.0520
  time to fit residues: 5.2754
Evaluate side-chains
  92 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  452 LEU
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   35 VAL
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue   63 ARG
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  113 ASP
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain H residue  126 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  40 GLN
H  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.132075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.109856 restraints weight = 5075.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.112589 restraints weight = 3368.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.114519 restraints weight = 2565.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.115666 restraints weight = 2121.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.116696 restraints weight = 1871.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3406  Z= 0.206
  Angle     :  0.707   9.614   4632  Z= 0.350
  Chirality :  0.047   0.193    492
  Planarity :  0.004   0.030    600
  Dihedral  :  5.253  22.235    476
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 23.10 %
    Favored  : 72.11 %
  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 are not related in a simple way.
  whole: -2.95 (0.41), residues: 419
  helix: -4.81 (0.44), residues: 20
  sheet: -1.40 (0.49), residues: 126
  loop : -2.10 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 346 
 TYR   0.038   0.002   TYR L  93 
 PHE   0.014   0.002   PHE F 338 
 TRP   0.019   0.002   TRP F 436 
 HIS   0.006   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00483 /  0.21 ( 3401)
  covalent geometry    : angle       0.68916 /  0.34 ( 4620)
  SS BOND              : bond        0.00419 /  0.21 (    3)
  SS BOND              : angle       4.31409 /  2.58 (    6)
  hydrogen bonds       : bond        0.03957 /  2.37 (   66)
  hydrogen bonds       : angle       6.10822 /  4.10 (  168)
  link_BETA1-4         : bond        0.00797 /  0.42 (    1)
  link_BETA1-4         : angle       1.10947 /  0.55 (    3)
  link_NAG-ASN         : bond        0.00206 /  0.11 (    1)
  link_NAG-ASN         : angle       0.95653 /  0.55 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.075 
Fit side-chains
REVERT: F  354 ASN cc_start: 0.8835 (p0) cc_final: 0.8480 (p0)
REVERT: F  427 ASP cc_start: 0.8282 (t0) cc_final: 0.7992 (t0)
REVERT: F  474 GLN cc_start: 0.5894 (tp40) cc_final: 0.5363 (tm-30)
REVERT: L   16 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8124 (mp10)
REVERT: H   16 ARG cc_start: 0.2320 (mmt180) cc_final: 0.1903 (mmt180)
  outliers start: 17
  outliers final: 16
  residues processed: 87
  average time/residue: 0.0671
  time to fit residues: 6.9122
Evaluate side-chains
  92 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  452 LEU
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   35 VAL
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue   63 ARG
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain H residue  127 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  40 GLN
H  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.134012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.112119 restraints weight = 5028.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.114868 restraints weight = 3351.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.116382 restraints weight = 2528.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.118060 restraints weight = 2124.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.118891 restraints weight = 1844.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3406  Z= 0.175
  Angle     :  0.689  10.089   4632  Z= 0.339
  Chirality :  0.047   0.182    492
  Planarity :  0.004   0.031    600
  Dihedral  :  5.219  22.322    476
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 22.82 %
    Favored  : 72.39 %
  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 are not related in a simple way.
  whole: -2.94 (0.41), residues: 419
  helix: -4.87 (0.43), residues: 20
  sheet: -1.40 (0.49), residues: 126
  loop : -2.08 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 346 
 TYR   0.044   0.002   TYR L  93 
 PHE   0.012   0.002   PHE F 429 
 TRP   0.015   0.001   TRP F 436 
 HIS   0.007   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00409 /  0.17 ( 3401)
  covalent geometry    : angle       0.67260 /  0.33 ( 4620)
  SS BOND              : bond        0.00263 /  0.13 (    3)
  SS BOND              : angle       4.11183 /  2.47 (    6)
  hydrogen bonds       : bond        0.03664 /  2.19 (   66)
  hydrogen bonds       : angle       6.07589 /  4.10 (  168)
  link_BETA1-4         : bond        0.00778 /  0.41 (    1)
  link_BETA1-4         : angle       1.08206 /  0.54 (    3)
  link_NAG-ASN         : bond        0.00109 /  0.06 (    1)
  link_NAG-ASN         : angle       0.88092 /  0.51 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.075 
Fit side-chains
REVERT: F  354 ASN cc_start: 0.8835 (p0) cc_final: 0.8487 (p0)
REVERT: F  474 GLN cc_start: 0.5903 (tp40) cc_final: 0.5369 (tm-30)
REVERT: L   16 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8094 (mp10)
REVERT: H   16 ARG cc_start: 0.2453 (mmt180) cc_final: 0.2053 (mmt180)
  outliers start: 17
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0511
  time to fit residues: 5.2677
Evaluate side-chains
  93 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  452 LEU
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   35 VAL
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue   63 ARG
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain H residue  127 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.0570
   chunk 35 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0770
   chunk 2 optimal weight:    0.2980
   chunk 24 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.3256

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 115 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.137794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.115829 restraints weight = 5094.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.118637 restraints weight = 3264.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.120760 restraints weight = 2451.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.122064 restraints weight = 1999.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.122696 restraints weight = 1738.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3406  Z= 0.125
  Angle     :  0.643   9.782   4632  Z= 0.314
  Chirality :  0.046   0.173    492
  Planarity :  0.004   0.031    600
  Dihedral  :  4.957  22.035    476
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 23.94 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.85 (0.41), residues: 419
  helix: -4.88 (0.43), residues: 20
  sheet: -1.39 (0.47), residues: 132
  loop : -1.99 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 346 
 TYR   0.038   0.002   TYR H 114 
 PHE   0.011   0.001   PHE F 456 
 TRP   0.010   0.001   TRP F 436 
 HIS   0.007   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 3401)
  covalent geometry    : angle       0.64082 /  0.31 ( 4620)
  SS BOND              : bond        0.00351 /  0.17 (    3)
  SS BOND              : angle       1.33344 /  0.78 (    6)
  hydrogen bonds       : bond        0.03175 /  1.91 (   66)
  hydrogen bonds       : angle       6.04432 /  4.14 (  168)
  link_BETA1-4         : bond        0.00790 /  0.42 (    1)
  link_BETA1-4         : angle       1.05921 /  0.53 (    3)
  link_NAG-ASN         : bond        0.00021 /  0.01 (    1)
  link_NAG-ASN         : angle       0.67981 /  0.39 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 888.77 seconds
wall clock time: 15 minutes 58.25 seconds (958.25 seconds total)