Starting phenix.real_space_refine
on Fri Aug 22 13:18:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gsb_34228/08_2025/8gsb_34228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gsb_34228/08_2025/8gsb_34228.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gsb_34228/08_2025/8gsb_34228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gsb_34228/08_2025/8gsb_34228.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gsb_34228/08_2025/8gsb_34228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gsb_34228/08_2025/8gsb_34228.map"
  }
  resolution = 3.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.038
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    2001      2.51       5
     N     544      2.21       5
     O     596      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 3157
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 173, 1404
          Classifications: {'peptide': 173}
          Link IDs: {'PTRANS': 8, 'TRANS': 164}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 933
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "K"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 820
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99}
  Time building chain proxies: 1.12, per 1000 atoms: 0.35
  Number of scatterers: 3157
  At special positions: 0
  Unit cell: (78.306, 60.624, 95.988, 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     596      8.00
     N     544      7.00
     C    2001      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " 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  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 101 " - pdb=" SG  CYS H 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  23 " - pdb=" SG  CYS K  89 " 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
  Time building additional restraints: 0.26
  Conformation dependent library (CDL) restraints added in 127.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  734

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 9 sheets defined
      4.2% alpha, 32.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 4.238A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'K' and resid 80 through 84
    Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 379
      removed outlier: 3.751A  pdb=" N   LYS A 378 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER A 514 " --> pdb=" O   TYR A 396 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 379
      removed outlier: 3.751A  pdb=" N   LYS A 378 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
      removed outlier: 3.632A  pdb=" N   ARG A 493 " --> pdb=" O   TYR A 453 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.743A  pdb=" N   THR H 120 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   VAL H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   TRP H  50 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TRP H  50 " --> pdb=" O   ASN H  59 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.743A  pdb=" N   THR H 120 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 5 through 7
      removed outlier: 3.527A  pdb=" N   THR K  66 " --> pdb=" O   THR K  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12
    Processing sheet with id=AA9, first strand: chain 'K' and resid 54 through 55
      removed outlier: 6.456A  pdb=" N   TRP K  36 " --> pdb=" O   LEU K  48 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   TYR K  50 " --> pdb=" O   LEU K  34 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU K  34 " --> pdb=" O   TYR K  50 " (cutoff:3.500A)

    92 hydrogen bonds defined for protein.
    204 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.48

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1010
        1.34 -     1.46: 819
        1.46 -     1.58: 1389
        1.58 -     1.70: 0
        1.70 -     1.82: 19
  Bond restraints: 3237
  Sorted by residual:
  bond pdb=" C   PRO K  81 "
       pdb=" N   GLU K  82 "
    ideal  model  delta    sigma   weight residual
    1.334  1.280  0.054 1.38e-02 5.25e+03 1.54e+01
  bond pdb=" C   LEU K  74 "
       pdb=" N   THR K  75 "
    ideal  model  delta    sigma   weight residual
    1.331  1.388 -0.057 1.55e-02 4.16e+03 1.33e+01
  bond pdb=" C   GLN K  90 "
       pdb=" N   GLN K  91 "
    ideal  model  delta    sigma   weight residual
    1.330  1.378 -0.048 1.39e-02 5.18e+03 1.19e+01
  bond pdb=" C   ALA A 419 "
       pdb=" N   ASP A 420 "
    ideal  model  delta    sigma   weight residual
    1.333  1.290  0.043 1.51e-02 4.39e+03 8.15e+00
  bond pdb=" C   GLU H  46 "
       pdb=" N   TRP H  47 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.31e-02 5.83e+03 7.24e+00
  ... (remaining 3232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 4246
        1.78 -     3.57: 125
        3.57 -     5.35: 17
        5.35 -     7.14: 2
        7.14 -     8.92: 4
  Bond angle restraints: 4394
  Sorted by residual:
  angle pdb=" N   GLN K  91 "
        pdb=" CA  GLN K  91 "
        pdb=" C   GLN K  91 "
      ideal   model   delta    sigma   weight residual
     109.24  100.32    8.92 1.63e+00 3.76e-01 3.00e+01
  angle pdb=" N   VAL A 341 "
        pdb=" CA  VAL A 341 "
        pdb=" C   VAL A 341 "
      ideal   model   delta    sigma   weight residual
     109.34  117.51   -8.17 2.08e+00 2.31e-01 1.54e+01
  angle pdb=" N   GLY A 476 "
        pdb=" CA  GLY A 476 "
        pdb=" C   GLY A 476 "
      ideal   model   delta    sigma   weight residual
     113.18  104.87    8.31 2.37e+00 1.78e-01 1.23e+01
  angle pdb=" N   PHE A 400 "
        pdb=" CA  PHE A 400 "
        pdb=" C   PHE A 400 "
      ideal   model   delta    sigma   weight residual
     108.99  114.35   -5.36 1.57e+00 4.06e-01 1.17e+01
  angle pdb=" N   GLN A 474 "
        pdb=" CA  GLN A 474 "
        pdb=" C   GLN A 474 "
      ideal   model   delta    sigma   weight residual
     110.80  118.07   -7.27 2.13e+00 2.20e-01 1.16e+01
  ... (remaining 4389 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.28: 1655
       14.28 -    28.56: 186
       28.56 -    42.85: 46
       42.85 -    57.13: 16
       57.13 -    71.41: 4
  Dihedral angle restraints: 1907
    sinusoidal: 752
      harmonic: 1155
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.88  -61.88     1      1.00e+01 1.00e-02 5.08e+01
  dihedral pdb=" CA  ALA A 475 "
           pdb=" C   ALA A 475 "
           pdb=" N   GLY A 476 "
           pdb=" CA  GLY A 476 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.37   25.63     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CB  CYS H 101 "
           pdb=" SG  CYS H 101 "
           pdb=" SG  CYS H 106 "
           pdb=" CB  CYS H 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  133.22  -40.22     1      1.00e+01 1.00e-02 2.27e+01
  ... (remaining 1904 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 385
       0.052 -    0.104: 61
       0.104 -    0.156: 20
       0.156 -    0.207: 0
       0.207 -    0.259: 1
  Chirality restraints: 467
  Sorted by residual:
  chirality pdb=" CA  GLN A 474 "
            pdb=" N   GLN A 474 "
            pdb=" C   GLN A 474 "
            pdb=" CB  GLN A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  VAL A 511 "
            pdb=" N   VAL A 511 "
            pdb=" C   VAL A 511 "
            pdb=" CB  VAL A 511 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.14e-01
  chirality pdb=" CA  VAL H 119 "
            pdb=" N   VAL H 119 "
            pdb=" C   VAL H 119 "
            pdb=" CB  VAL H 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.71e-01
  ... (remaining 464 not shown)

  Planarity restraints: 569
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  44 "   -0.181 9.50e-02 1.11e+02   8.12e-02 4.43e+00
        pdb=" NE  ARG H  44 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  44 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  44 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  44 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER K   7 "    0.032 5.00e-02 4.00e+02   4.91e-02 3.86e+00
        pdb=" N   PRO K   8 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO K   8 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO K   8 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 492 "    0.009 2.00e-02 2.50e+03   1.83e-02 3.36e+00
        pdb=" C   LEU A 492 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   LEU A 492 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A 493 "    0.011 2.00e-02 2.50e+03
  ... (remaining 566 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1168
        2.85 -     3.36: 2819
        3.36 -     3.88: 4750
        3.88 -     4.39: 5283
        4.39 -     4.90: 9213
  Nonbonded interactions: 23233
  Sorted by model distance:
  nonbonded pdb=" O   GLY H  26 "
            pdb=" OG1 THR H  30 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   GLN A 474 "
            pdb=" O   ASN A 487 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" O   SER A 514 "
            pdb=" OG  SER A 514 "
     model   vdw
     2.395 3.040
  nonbonded pdb=" O   ASP K  61 "
            pdb=" OD1 ASP K  61 "
     model   vdw
     2.406 3.040
  nonbonded pdb=" O   ASP A 339 "
            pdb=" OD1 ASP A 339 "
     model   vdw
     2.414 3.040
  ... (remaining 23228 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     5.570
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
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      :  0.004   0.057   3242  Z= 0.245
  Angle     :  0.728   8.922   4404  Z= 0.429
  Chirality :  0.045   0.259    467
  Planarity :  0.005   0.081    569
  Dihedral  : 13.337  71.409   1158
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.42 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.42), residues: 392
  helix: -3.19 (1.17), residues: 8
  sheet: -0.89 (0.49), residues: 119
  loop : -1.36 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  44 
 TYR   0.027   0.002   TYR K  92 
 PHE   0.011   0.001   PHE A 486 
 TRP   0.013   0.002   TRP K  97 
 HIS   0.001   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 3237)
  covalent geometry    : angle       0.72832 ( 4394)
  SS BOND              : bond        0.00171 (    5)
  SS BOND              : angle       0.80340 (   10)
  hydrogen bonds       : bond        0.26585 (   80)
  hydrogen bonds       : angle       9.55811 (  204)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A  474 GLN cc_start: 0.7006 (tp-100) cc_final: 0.6602 (tp-100)
REVERT: H   47 TRP cc_start: 0.8813 (t60) cc_final: 0.8190 (t60)
REVERT: K    8 PRO cc_start: 0.8518 (Cg_exo) cc_final: 0.8287 (Cg_endo)
REVERT: K   33 TYR cc_start: 0.7996 (m-10) cc_final: 0.7768 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1128
  time to fit residues: 9.8747
Evaluate side-chains
  64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0270
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0970
   overall best weight:    0.8038

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.125010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.105254 restraints weight = 6663.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.106302 restraints weight = 5101.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.107291 restraints weight = 4614.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.107671 restraints weight = 3532.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.107842 restraints weight = 3422.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3242  Z= 0.145
  Angle     :  0.621   8.837   4404  Z= 0.330
  Chirality :  0.044   0.137    467
  Planarity :  0.004   0.042    569
  Dihedral  :  4.911  24.314    447
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.62 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.42), residues: 392
  helix: -4.13 (0.88), residues: 14
  sheet: -0.73 (0.48), residues: 126
  loop : -0.94 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  44 
 TYR   0.026   0.002   TYR K  92 
 PHE   0.019   0.002   PHE K  72 
 TRP   0.013   0.002   TRP K  97 
 HIS   0.001   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3237)
  covalent geometry    : angle       0.61919 ( 4394)
  SS BOND              : bond        0.00272 (    5)
  SS BOND              : angle       1.05391 (   10)
  hydrogen bonds       : bond        0.03026 (   80)
  hydrogen bonds       : angle       6.50945 (  204)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A  442 ASP cc_start: 0.8244 (m-30) cc_final: 0.7956 (t0)
REVERT: H   47 TRP cc_start: 0.8762 (t60) cc_final: 0.8252 (t60)
REVERT: H   57 ASN cc_start: 0.8296 (t0) cc_final: 0.7874 (t0)
REVERT: K  106 GLU cc_start: 0.6650 (pm20) cc_final: 0.6415 (pm20)
  outliers start: 6
  outliers final: 1
  residues processed: 78
  average time/residue: 0.1085
  time to fit residues: 9.6449
Evaluate side-chains
  65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 34 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 4 optimal weight:    0.3980
   chunk 14 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.4788

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 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 = 0.3600 r_free = 0.3600 target = 0.120658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.101176 restraints weight = 6583.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.100987 restraints weight = 5368.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.101765 restraints weight = 5679.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.102126 restraints weight = 4505.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.103054 restraints weight = 4079.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3242  Z= 0.215
  Angle     :  0.655   8.115   4404  Z= 0.348
  Chirality :  0.045   0.145    467
  Planarity :  0.005   0.037    569
  Dihedral  :  5.241  24.881    447
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.54 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.41), residues: 392
  helix: -4.15 (0.84), residues: 14
  sheet: -0.95 (0.45), residues: 130
  loop : -1.12 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  19 
 TYR   0.032   0.002   TYR K  92 
 PHE   0.014   0.002   PHE A 400 
 TRP   0.011   0.002   TRP K  36 
 HIS   0.002   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 3237)
  covalent geometry    : angle       0.65290 ( 4394)
  SS BOND              : bond        0.00259 (    5)
  SS BOND              : angle       1.17430 (   10)
  hydrogen bonds       : bond        0.03525 (   80)
  hydrogen bonds       : angle       6.09502 (  204)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASP cc_start: 0.8281 (m-30) cc_final: 0.8029 (m-30)
REVERT: A  442 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8077 (t0)
REVERT: H   47 TRP cc_start: 0.8951 (t60) cc_final: 0.8527 (t60)
REVERT: H   57 ASN cc_start: 0.8440 (t0) cc_final: 0.8113 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 68
  average time/residue: 0.0936
  time to fit residues: 7.4055
Evaluate side-chains
  66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain K residue   48 LEU
Chi-restraints excluded: chain K residue   62 ARG
Chi-restraints excluded: chain K residue   98 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    0.0770
   chunk 31 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0970
   chunk 8 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.4536

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 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 = 0.3654 r_free = 0.3654 target = 0.123838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.103431 restraints weight = 6395.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.104199 restraints weight = 5091.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.104663 restraints weight = 4358.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.105664 restraints weight = 3786.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.106135 restraints weight = 3238.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3242  Z= 0.118
  Angle     :  0.593   8.441   4404  Z= 0.308
  Chirality :  0.043   0.134    467
  Planarity :  0.004   0.038    569
  Dihedral  :  4.617  22.388    447
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.41 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (0.41), residues: 392
  helix: -4.22 (0.86), residues: 15
  sheet: -0.79 (0.46), residues: 125
  loop : -1.01 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  44 
 TYR   0.023   0.002   TYR K  92 
 PHE   0.008   0.001   PHE A 392 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3237)
  covalent geometry    : angle       0.59228 ( 4394)
  SS BOND              : bond        0.00248 (    5)
  SS BOND              : angle       0.98377 (   10)
  hydrogen bonds       : bond        0.02601 (   80)
  hydrogen bonds       : angle       5.28408 (  204)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASP cc_start: 0.8316 (m-30) cc_final: 0.8035 (m-30)
REVERT: H   10 GLU cc_start: 0.6937 (mp0) cc_final: 0.6705 (mp0)
REVERT: H   47 TRP cc_start: 0.8784 (t60) cc_final: 0.8360 (t60)
REVERT: H   57 ASN cc_start: 0.8256 (t0) cc_final: 0.7883 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 82
  average time/residue: 0.0934
  time to fit residues: 8.9625
Evaluate side-chains
  72 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain K residue   48 LEU
Chi-restraints excluded: chain K residue   62 ARG
Chi-restraints excluded: chain K residue   98 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0970
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0770
   overall best weight:    0.6538

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.123240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.102928 restraints weight = 6380.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.103893 restraints weight = 5186.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.104198 restraints weight = 4276.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.105474 restraints weight = 3756.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.105606 restraints weight = 3129.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3242  Z= 0.126
  Angle     :  0.590   8.044   4404  Z= 0.308
  Chirality :  0.043   0.133    467
  Planarity :  0.004   0.035    569
  Dihedral  :  4.577  22.156    447
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 16.03 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.42), residues: 392
  helix: -4.20 (0.85), residues: 15
  sheet: -0.70 (0.46), residues: 129
  loop : -0.99 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  44 
 TYR   0.023   0.001   TYR K  92 
 PHE   0.009   0.001   PHE A 400 
 TRP   0.007   0.001   TRP K  36 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3237)
  covalent geometry    : angle       0.58888 ( 4394)
  SS BOND              : bond        0.00225 (    5)
  SS BOND              : angle       0.94689 (   10)
  hydrogen bonds       : bond        0.02696 (   80)
  hydrogen bonds       : angle       5.00240 (  204)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASP cc_start: 0.8321 (m-30) cc_final: 0.7989 (m-30)
REVERT: A  474 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7562 (tm-30)
REVERT: H   10 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6319 (mp0)
REVERT: H   47 TRP cc_start: 0.8801 (t60) cc_final: 0.8499 (t60)
REVERT: H   57 ASN cc_start: 0.8321 (t0) cc_final: 0.7986 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 76
  average time/residue: 0.0919
  time to fit residues: 8.1350
Evaluate side-chains
  71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   93 CYS
Chi-restraints excluded: chain K residue   48 LEU
Chi-restraints excluded: chain K residue   89 CYS
Chi-restraints excluded: chain K residue   98 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0570
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0770
   chunk 4 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6060

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

Flipped N/Q/H residues before XYZ refinement:
K  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.124051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.104453 restraints weight = 6632.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.104744 restraints weight = 5477.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.105511 restraints weight = 5001.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.105973 restraints weight = 4209.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.106182 restraints weight = 3799.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3242  Z= 0.125
  Angle     :  0.590   8.004   4404  Z= 0.310
  Chirality :  0.043   0.130    467
  Planarity :  0.004   0.034    569
  Dihedral  :  4.529  22.253    447
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.33 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.42), residues: 392
  helix: -4.30 (0.76), residues: 15
  sheet: -0.63 (0.46), residues: 129
  loop : -0.95 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  44 
 TYR   0.018   0.001   TYR K  92 
 PHE   0.007   0.001   PHE K  63 
 TRP   0.006   0.001   TRP K  36 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3237)
  covalent geometry    : angle       0.58973 ( 4394)
  SS BOND              : bond        0.00200 (    5)
  SS BOND              : angle       0.85655 (   10)
  hydrogen bonds       : bond        0.02531 (   80)
  hydrogen bonds       : angle       4.79579 (  204)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASP cc_start: 0.8245 (m-30) cc_final: 0.7966 (m-30)
REVERT: A  474 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7510 (tm-30)
REVERT: H   10 GLU cc_start: 0.6722 (mp0) cc_final: 0.6307 (mp0)
REVERT: H   47 TRP cc_start: 0.8816 (t60) cc_final: 0.8550 (t60)
REVERT: H   57 ASN cc_start: 0.8303 (t0) cc_final: 0.7966 (t0)
REVERT: K   39 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7952 (tt0)
  outliers start: 10
  outliers final: 8
  residues processed: 77
  average time/residue: 0.1014
  time to fit residues: 9.0235
Evaluate side-chains
  76 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   93 CYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain K residue   39 GLN
Chi-restraints excluded: chain K residue   89 CYS
Chi-restraints excluded: chain K residue   98 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 34 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
** K   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.120656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.099948 restraints weight = 6550.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.100216 restraints weight = 4787.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.100803 restraints weight = 4921.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.101145 restraints weight = 4080.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.102524 restraints weight = 3655.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3242  Z= 0.185
  Angle     :  0.650   8.224   4404  Z= 0.344
  Chirality :  0.044   0.145    467
  Planarity :  0.005   0.057    569
  Dihedral  :  4.859  22.808    447
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 15.74 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.42), residues: 392
  helix: -4.37 (0.70), residues: 15
  sheet: -0.72 (0.46), residues: 129
  loop : -0.99 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  44 
 TYR   0.021   0.002   TYR A 423 
 PHE   0.018   0.002   PHE A 400 
 TRP   0.011   0.001   TRP K  36 
 HIS   0.001   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 3237)
  covalent geometry    : angle       0.64643 ( 4394)
  SS BOND              : bond        0.00341 (    5)
  SS BOND              : angle       1.55800 (   10)
  hydrogen bonds       : bond        0.02972 (   80)
  hydrogen bonds       : angle       4.99747 (  204)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASP cc_start: 0.8352 (m-30) cc_final: 0.7948 (m-30)
REVERT: H   10 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6413 (mp0)
REVERT: H   47 TRP cc_start: 0.8948 (t60) cc_final: 0.8582 (t60)
REVERT: K   61 ASP cc_start: 0.7205 (t0) cc_final: 0.6883 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 79
  average time/residue: 0.0937
  time to fit residues: 8.5770
Evaluate side-chains
  75 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   93 CYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain K residue   48 LEU
Chi-restraints excluded: chain K residue   89 CYS
Chi-restraints excluded: chain K residue   98 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 4 optimal weight:    0.0470
   chunk 14 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 36 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
K  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.122506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.101612 restraints weight = 6723.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.102074 restraints weight = 4847.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.102652 restraints weight = 4704.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.102924 restraints weight = 4068.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.103243 restraints weight = 3644.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.3578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3242  Z= 0.139
  Angle     :  0.641   7.696   4404  Z= 0.336
  Chirality :  0.043   0.133    467
  Planarity :  0.004   0.034    569
  Dihedral  :  4.564  21.488    447
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 16.91 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.42), residues: 392
  helix: -4.37 (0.72), residues: 15
  sheet: -0.69 (0.46), residues: 130
  loop : -0.91 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  44 
 TYR   0.016   0.001   TYR K  92 
 PHE   0.010   0.001   PHE A 400 
 TRP   0.007   0.001   TRP K  36 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3237)
  covalent geometry    : angle       0.63897 ( 4394)
  SS BOND              : bond        0.00235 (    5)
  SS BOND              : angle       1.22439 (   10)
  hydrogen bonds       : bond        0.02637 (   80)
  hydrogen bonds       : angle       4.72685 (  204)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  405 ASP cc_start: 0.8350 (m-30) cc_final: 0.7963 (m-30)
REVERT: H   10 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6780 (mp0)
REVERT: H   47 TRP cc_start: 0.8888 (t60) cc_final: 0.8615 (t60)
REVERT: K   39 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7968 (tt0)
REVERT: K   61 ASP cc_start: 0.7236 (t0) cc_final: 0.6881 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0953
  time to fit residues: 8.6074
Evaluate side-chains
  77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   93 CYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain K residue   39 GLN
Chi-restraints excluded: chain K residue   89 CYS
Chi-restraints excluded: chain K residue   98 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0000
   chunk 25 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
** K   6 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 = 0.3627 r_free = 0.3627 target = 0.122431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.099032 restraints weight = 6474.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.101349 restraints weight = 4575.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.103074 restraints weight = 3586.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.104151 restraints weight = 3006.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.105069 restraints weight = 2666.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3242  Z= 0.134
  Angle     :  0.641   8.192   4404  Z= 0.336
  Chirality :  0.043   0.130    467
  Planarity :  0.004   0.034    569
  Dihedral  :  4.540  21.545    447
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 16.33 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.41 (0.42), residues: 392
  helix: -4.43 (0.66), residues: 15
  sheet: -0.62 (0.47), residues: 130
  loop : -0.86 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  44 
 TYR   0.015   0.001   TYR K  92 
 PHE   0.010   0.001   PHE A 400 
 TRP   0.006   0.001   TRP H  50 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3237)
  covalent geometry    : angle       0.64007 ( 4394)
  SS BOND              : bond        0.00209 (    5)
  SS BOND              : angle       1.08037 (   10)
  hydrogen bonds       : bond        0.02632 (   80)
  hydrogen bonds       : angle       4.67880 (  204)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  405 ASP cc_start: 0.8340 (m-30) cc_final: 0.7922 (m-30)
REVERT: H   47 TRP cc_start: 0.8839 (t60) cc_final: 0.8481 (t60)
REVERT: K   61 ASP cc_start: 0.7324 (t0) cc_final: 0.6970 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0977
  time to fit residues: 8.6364
Evaluate side-chains
  74 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue   93 CYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain K residue   89 CYS
Chi-restraints excluded: chain K residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0770
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.123166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.103300 restraints weight = 6683.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.103383 restraints weight = 5624.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.104178 restraints weight = 5016.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.105035 restraints weight = 4236.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.105186 restraints weight = 3811.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3242  Z= 0.141
  Angle     :  0.677   8.809   4404  Z= 0.353
  Chirality :  0.044   0.159    467
  Planarity :  0.004   0.033    569
  Dihedral  :  4.609  21.162    447
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.91 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.42), residues: 392
  helix: -4.27 (0.63), residues: 21
  sheet: -0.44 (0.47), residues: 127
  loop : -0.88 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  44 
 TYR   0.017   0.001   TYR H  80 
 PHE   0.008   0.001   PHE A 400 
 TRP   0.007   0.001   TRP H  50 
 HIS   0.001   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3237)
  covalent geometry    : angle       0.67640 ( 4394)
  SS BOND              : bond        0.00156 (    5)
  SS BOND              : angle       1.04009 (   10)
  hydrogen bonds       : bond        0.02665 (   80)
  hydrogen bonds       : angle       4.58819 (  204)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 TRP cc_start: 0.8832 (t60) cc_final: 0.8549 (t60)
REVERT: K   61 ASP cc_start: 0.7157 (t0) cc_final: 0.6799 (t0)
  outliers start: 11
  outliers final: 10
  residues processed: 76
  average time/residue: 0.1028
  time to fit residues: 9.0144
Evaluate side-chains
  76 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue   93 CYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain K residue   48 LEU
Chi-restraints excluded: chain K residue   89 CYS
Chi-restraints excluded: chain K residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** K   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.123025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.101823 restraints weight = 6646.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.102269 restraints weight = 4709.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.103148 restraints weight = 4897.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.103910 restraints weight = 3754.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.104335 restraints weight = 3471.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3242  Z= 0.149
  Angle     :  0.672   9.126   4404  Z= 0.351
  Chirality :  0.044   0.159    467
  Planarity :  0.004   0.033    569
  Dihedral  :  4.664  20.885    447
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 17.78 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.42), residues: 392
  helix: -4.20 (0.68), residues: 21
  sheet: -0.48 (0.47), residues: 127
  loop : -0.90 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  44 
 TYR   0.019   0.001   TYR H  80 
 PHE   0.010   0.001   PHE A 400 
 TRP   0.007   0.001   TRP H  50 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3237)
  covalent geometry    : angle       0.67071 ( 4394)
  SS BOND              : bond        0.00194 (    5)
  SS BOND              : angle       1.08101 (   10)
  hydrogen bonds       : bond        0.02791 (   80)
  hydrogen bonds       : angle       4.63290 (  204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 908.77 seconds
wall clock time: 16 minutes 21.80 seconds (981.80 seconds total)