Starting phenix.real_space_refine
on Fri Aug 22 15:19:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k5g_36905/08_2025/8k5g_36905.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k5g_36905/08_2025/8k5g_36905.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k5g_36905/08_2025/8k5g_36905.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k5g_36905/08_2025/8k5g_36905.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k5g_36905/08_2025/8k5g_36905.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k5g_36905/08_2025/8k5g_36905.map"
  }
  resolution = 3.41
  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=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1744 atoms to isotropic.
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      18      5.16       5
     C    2152      2.51       5
     N     574      2.21       5
     O     637      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3381
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 948
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
    Chain: "L"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 816
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99}
    Chain: "A"
      Number of atoms: 1617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1617
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 13, 'TRANS': 187}
  Time building chain proxies: 0.96, per 1000 atoms: 0.28
  Number of scatterers: 3381
  At special positions: 0
  Unit cell: (60.3, 113.9, 75.04, 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      18     16.00
     O     637      8.00
     N     574      7.00
     C    2152      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    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 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 358 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 429 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 388 " - pdb=" SG  CYS A 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 477 " - pdb=" SG  CYS A 485 " 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: 0.18
  Conformation dependent library (CDL) restraints added in 94.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 8 sheets defined
      6.3% alpha, 32.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 4.024A  pdb=" N   THR H  91 " --> pdb=" O   PHE H  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 350
      removed outlier: 3.802A  pdb=" N   TRP A 350 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 366
      removed outlier: 3.524A  pdb=" N   LEU A 365 " --> pdb=" O   TYR A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 408
      removed outlier: 3.918A  pdb=" N   ALA A 408 " --> pdb=" O   ARG A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 419
      removed outlier: 3.995A  pdb=" N   TYR A 418 " --> pdb=" O   ASN A 414 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.731A  pdb=" N   VAL H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   TRP H  50 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7
      removed outlier: 4.562A  pdb=" N   PHE L  72 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ASP L  71 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 11
      removed outlier: 6.689A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 355
      removed outlier: 3.637A  pdb=" N   ASN A 351 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 392 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A 521 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   CYS A 358 " --> pdb=" O   CYS A 522 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355
      removed outlier: 3.637A  pdb=" N   ASN A 351 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 392 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
      removed outlier: 5.443A  pdb=" N   ASN A 391 " --> pdb=" O   GLU A 513 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   GLU A 513 " --> pdb=" O   ASN A 391 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLY A 401 " --> pdb=" O   GLN A 503 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   GLN A 503 " --> pdb=" O   GLY A 401 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451

    94 hydrogen bonds defined for protein.
    216 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: 0.44

  Time building geometry restraints manager: 0.25 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1084
        1.35 -     1.46: 908
        1.46 -     1.58: 1456
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 3470
  Sorted by residual:
  bond pdb=" N   VAL A 442 "
       pdb=" CA  VAL A 442 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.013 1.25e-02 6.40e+03 1.05e+00
  bond pdb=" CA  SER A 443 "
       pdb=" C   SER A 443 "
    ideal  model  delta    sigma   weight residual
    1.519  1.513  0.005 5.30e-03 3.56e+04 9.61e-01
  bond pdb=" CA  CYS A 333 "
       pdb=" CB  CYS A 333 "
    ideal  model  delta    sigma   weight residual
    1.536  1.524  0.012 1.25e-02 6.40e+03 8.56e-01
  bond pdb=" CB  CYS A 358 "
       pdb=" SG  CYS A 358 "
    ideal  model  delta    sigma   weight residual
    1.808  1.778  0.030 3.30e-02 9.18e+02 8.12e-01
  bond pdb=" CG  PRO L  96 "
       pdb=" CD  PRO L  96 "
    ideal  model  delta    sigma   weight residual
    1.512  1.488  0.024 2.70e-02 1.37e+03 7.86e-01
  ... (remaining 3465 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 4613
        2.00 -     4.00: 91
        4.00 -     6.00: 5
        6.00 -     8.00: 2
        8.00 -    10.01: 2
  Bond angle restraints: 4713
  Sorted by residual:
  angle pdb=" C   LYS A 441 "
        pdb=" N   VAL A 442 "
        pdb=" CA  VAL A 442 "
      ideal   model   delta    sigma   weight residual
     121.97  131.98  -10.01 1.80e+00 3.09e-01 3.09e+01
  angle pdb=" CA  SER A 443 "
        pdb=" C   SER A 443 "
        pdb=" N   GLY A 444 "
      ideal   model   delta    sigma   weight residual
     119.56  116.68    2.88 5.80e-01 2.97e+00 2.46e+01
  angle pdb=" N   VAL A 442 "
        pdb=" CA  VAL A 442 "
        pdb=" CB  VAL A 442 "
      ideal   model   delta    sigma   weight residual
     111.23  116.46   -5.23 1.65e+00 3.67e-01 1.01e+01
  angle pdb=" N   SER A 443 "
        pdb=" CA  SER A 443 "
        pdb=" C   SER A 443 "
      ideal   model   delta    sigma   weight residual
     108.12  112.89   -4.77 1.59e+00 3.96e-01 9.00e+00
  angle pdb=" N   PHE A 335 "
        pdb=" CA  PHE A 335 "
        pdb=" C   PHE A 335 "
      ideal   model   delta    sigma   weight residual
     112.88  109.15    3.73 1.29e+00 6.01e-01 8.38e+00
  ... (remaining 4708 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 1843
       17.57 -    35.15: 173
       35.15 -    52.72: 31
       52.72 -    70.29: 5
       70.29 -    87.87: 3
  Dihedral angle restraints: 2055
    sinusoidal: 809
      harmonic: 1246
  Sorted by residual:
  dihedral pdb=" CB  CYS A 477 "
           pdb=" SG  CYS A 477 "
           pdb=" SG  CYS A 485 "
           pdb=" CB  CYS A 485 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.13  -87.87     1      1.00e+01 1.00e-02 9.24e+01
  dihedral pdb=" CA  CYS A 358 "
           pdb=" C   CYS A 358 "
           pdb=" N   VAL A 359 "
           pdb=" CA  VAL A 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.20   26.80     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  PRO A 334 "
           pdb=" C   PRO A 334 "
           pdb=" N   PHE A 335 "
           pdb=" CA  PHE A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.40   21.60     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 2052 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.027: 259
       0.027 -    0.054: 145
       0.054 -    0.081: 51
       0.081 -    0.107: 26
       0.107 -    0.134: 20
  Chirality restraints: 501
  Sorted by residual:
  chirality pdb=" CA  PRO A 334 "
            pdb=" N   PRO A 334 "
            pdb=" C   PRO A 334 "
            pdb=" CB  PRO A 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.50e-01
  chirality pdb=" CA  ASN A 391 "
            pdb=" N   ASN A 391 "
            pdb=" C   ASN A 391 "
            pdb=" CB  ASN A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  VAL A 508 "
            pdb=" N   VAL A 508 "
            pdb=" C   VAL A 508 "
            pdb=" CB  VAL A 508 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 498 not shown)

  Planarity restraints: 611
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 441 "   -0.009 2.00e-02 2.50e+03   1.85e-02 3.41e+00
        pdb=" C   LYS A 441 "    0.032 2.00e-02 2.50e+03
        pdb=" O   LYS A 441 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A 442 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 369 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO A 370 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 370 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 370 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 517 "    0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO A 518 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 518 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 518 "    0.023 5.00e-02 4.00e+02
  ... (remaining 608 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 553
        2.77 -     3.30: 2862
        3.30 -     3.83: 4873
        3.83 -     4.37: 5694
        4.37 -     4.90: 10813
  Nonbonded interactions: 24795
  Sorted by model distance:
  nonbonded pdb=" O   SER A 443 "
            pdb=" NH1 ARG A 495 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" NH1 ARG A 454 "
            pdb=" OD2 ASP A 464 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" NE2 GLN L  39 "
            pdb=" O   GLN L  43 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" NH2 ARG A 451 "
            pdb=" O   SER A 466 "
     model   vdw
     2.367 3.120
  nonbonded pdb=" OG  SER H 106 "
            pdb=" OD2 ASP H 110 "
     model   vdw
     2.380 3.040
  ... (remaining 24790 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.560
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3477  Z= 0.137
  Angle     :  0.656  10.006   4727  Z= 0.354
  Chirality :  0.045   0.134    501
  Planarity :  0.004   0.043    611
  Dihedral  : 13.665  78.415   1242
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.00 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.07 (0.40), residues: 425
  helix: -5.08 (0.53), residues: 8
  sheet: -0.52 (0.46), residues: 150
  loop : -1.85 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 506 
 TYR   0.007   0.001   TYR L  92 
 PHE   0.005   0.001   PHE L  99 
 TRP   0.009   0.001   TRP A 350 
 HIS   0.002   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3470)
  covalent geometry    : angle       0.65364 ( 4713)
  SS BOND              : bond        0.00392 (    7)
  SS BOND              : angle       1.15166 (   14)
  hydrogen bonds       : bond        0.18109 (   83)
  hydrogen bonds       : angle       8.37344 (  216)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.084 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7070 (mt-10)
REVERT: H   73 ASP cc_start: 0.8043 (t70) cc_final: 0.7605 (t0)
REVERT: H   87 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7756 (mtm180)
REVERT: L    5 THR cc_start: 0.9000 (m) cc_final: 0.8764 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0823
  time to fit residues: 7.9375
Evaluate side-chains
  64 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
L   6 GLN
A 391 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.086527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.067846 restraints weight = 7507.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 3.55
r_work: 0.2726 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3477  Z= 0.173
  Angle     :  0.667  11.508   4727  Z= 0.341
  Chirality :  0.045   0.141    501
  Planarity :  0.004   0.044    611
  Dihedral  :  5.014  28.131    478
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.71 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  8.72 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.07 (0.41), residues: 425
  helix: -5.27 (0.33), residues: 14
  sheet: -0.29 (0.47), residues: 146
  loop : -1.88 (0.36), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  46 
 TYR   0.016   0.001   TYR L  50 
 PHE   0.007   0.001   PHE L  99 
 TRP   0.009   0.001   TRP A 433 
 HIS   0.002   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 3470)
  covalent geometry    : angle       0.66386 ( 4713)
  SS BOND              : bond        0.00423 (    7)
  SS BOND              : angle       1.28571 (   14)
  hydrogen bonds       : bond        0.03231 (   83)
  hydrogen bonds       : angle       6.22522 (  216)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.130 
Fit side-chains
REVERT: H   73 ASP cc_start: 0.8285 (t70) cc_final: 0.7583 (t0)
REVERT: H   87 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7766 (mtm110)
REVERT: H  100 TYR cc_start: 0.8756 (t80) cc_final: 0.8542 (t80)
REVERT: L    5 THR cc_start: 0.9017 (m) cc_final: 0.8685 (p)
REVERT: L   61 ASP cc_start: 0.8521 (t70) cc_final: 0.8299 (t70)
REVERT: A  337 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8149 (tm-30)
REVERT: A  386 ASP cc_start: 0.8673 (t0) cc_final: 0.8398 (t0)
REVERT: A  430 VAL cc_start: 0.9358 (OUTLIER) cc_final: 0.9088 (t)
  outliers start: 7
  outliers final: 3
  residues processed: 70
  average time/residue: 0.0711
  time to fit residues: 5.9572
Evaluate side-chains
  67 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain A residue  430 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    0.0970
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0040
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
H  62 GLN
L 101 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.088246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.068543 restraints weight = 7448.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 3.70
r_work: 0.2750 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3477  Z= 0.119
  Angle     :  0.614  11.632   4727  Z= 0.310
  Chirality :  0.044   0.140    501
  Planarity :  0.004   0.045    611
  Dihedral  :  4.735  26.826    478
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.76 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 11.17 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.06 (0.40), residues: 425
  helix: -5.29 (0.25), residues: 20
  sheet: -0.16 (0.48), residues: 144
  loop : -1.84 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  46 
 TYR   0.009   0.001   TYR A 505 
 PHE   0.006   0.001   PHE A 397 
 TRP   0.008   0.001   TRP A 350 
 HIS   0.001   0.000   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3470)
  covalent geometry    : angle       0.61278 ( 4713)
  SS BOND              : bond        0.00325 (    7)
  SS BOND              : angle       0.97689 (   14)
  hydrogen bonds       : bond        0.02767 (   83)
  hydrogen bonds       : angle       5.79933 (  216)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.134 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8211 (mt-10)
REVERT: H   73 ASP cc_start: 0.8236 (t70) cc_final: 0.7526 (t0)
REVERT: H   87 ARG cc_start: 0.8089 (mtm-85) cc_final: 0.7782 (mtm110)
REVERT: H   91 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7863 (t)
REVERT: H  100 TYR cc_start: 0.8693 (t80) cc_final: 0.8492 (t80)
REVERT: L    5 THR cc_start: 0.9002 (m) cc_final: 0.8612 (p)
REVERT: L   80 GLU cc_start: 0.7149 (mp0) cc_final: 0.6852 (mp0)
REVERT: A  337 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8056 (tm-30)
REVERT: A  386 ASP cc_start: 0.8706 (t0) cc_final: 0.8374 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 73
  average time/residue: 0.0697
  time to fit residues: 6.0800
Evaluate side-chains
  70 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0170
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
H  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.087553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.068106 restraints weight = 7390.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 3.64
r_work: 0.2739 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3477  Z= 0.126
  Angle     :  0.614  11.805   4727  Z= 0.308
  Chirality :  0.043   0.131    501
  Planarity :  0.004   0.047    611
  Dihedral  :  4.670  26.243    478
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.00 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 12.53 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.93 (0.40), residues: 425
  helix: -5.28 (0.25), residues: 20
  sheet:  0.12 (0.48), residues: 138
  loop : -1.83 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.008   0.001   TYR A 505 
 PHE   0.005   0.001   PHE L  99 
 TRP   0.007   0.001   TRP A 350 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3470)
  covalent geometry    : angle       0.61272 ( 4713)
  SS BOND              : bond        0.00359 (    7)
  SS BOND              : angle       1.00963 (   14)
  hydrogen bonds       : bond        0.02696 (   83)
  hydrogen bonds       : angle       5.69478 (  216)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.137 
Fit side-chains
REVERT: H   73 ASP cc_start: 0.8358 (t70) cc_final: 0.7590 (t0)
REVERT: H   87 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7709 (mtm110)
REVERT: H   91 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8067 (t)
REVERT: H  100 TYR cc_start: 0.8669 (t80) cc_final: 0.8462 (t80)
REVERT: L    5 THR cc_start: 0.9011 (m) cc_final: 0.8614 (p)
REVERT: A  337 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: A  386 ASP cc_start: 0.8734 (t0) cc_final: 0.8411 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0965
  time to fit residues: 8.1070
Evaluate side-chains
  73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
H  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.086701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.067751 restraints weight = 7356.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 3.55
r_work: 0.2729 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3477  Z= 0.151
  Angle     :  0.640  11.836   4727  Z= 0.322
  Chirality :  0.044   0.129    501
  Planarity :  0.004   0.047    611
  Dihedral  :  4.748  26.978    478
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.47 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 14.17 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.93 (0.40), residues: 425
  helix: -5.29 (0.25), residues: 20
  sheet:  0.17 (0.48), residues: 138
  loop : -1.86 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  46 
 TYR   0.007   0.001   TYR A 492 
 PHE   0.006   0.001   PHE L  99 
 TRP   0.008   0.001   TRP A 350 
 HIS   0.002   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3470)
  covalent geometry    : angle       0.63768 ( 4713)
  SS BOND              : bond        0.00390 (    7)
  SS BOND              : angle       1.15424 (   14)
  hydrogen bonds       : bond        0.02799 (   83)
  hydrogen bonds       : angle       5.63993 (  216)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.139 
Fit side-chains
REVERT: H   73 ASP cc_start: 0.8358 (t70) cc_final: 0.7583 (t0)
REVERT: H   87 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7927 (mtm110)
REVERT: H   91 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8136 (t)
REVERT: L    5 THR cc_start: 0.9050 (m) cc_final: 0.8665 (p)
REVERT: L   21 LEU cc_start: 0.9048 (mt) cc_final: 0.8794 (mp)
REVERT: L   61 ASP cc_start: 0.8791 (p0) cc_final: 0.8497 (t70)
REVERT: L   80 GLU cc_start: 0.7510 (mp0) cc_final: 0.7251 (mp0)
REVERT: A  337 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: A  386 ASP cc_start: 0.8768 (t0) cc_final: 0.8423 (t0)
REVERT: A  430 VAL cc_start: 0.9379 (OUTLIER) cc_final: 0.9102 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0869
  time to fit residues: 7.3524
Evaluate side-chains
  74 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3213 r_free = 0.3213 target = 0.086511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.066854 restraints weight = 7512.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 3.69
r_work: 0.2721 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3477  Z= 0.138
  Angle     :  0.629  11.948   4727  Z= 0.315
  Chirality :  0.044   0.128    501
  Planarity :  0.004   0.047    611
  Dihedral  :  4.726  26.792    478
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.47 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 14.71 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.94 (0.40), residues: 425
  helix: -5.28 (0.25), residues: 20
  sheet:  0.14 (0.48), residues: 138
  loop : -1.86 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  46 
 TYR   0.018   0.001   TYR H 100 
 PHE   0.005   0.001   PHE L  99 
 TRP   0.008   0.001   TRP A 350 
 HIS   0.002   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3470)
  covalent geometry    : angle       0.62714 ( 4713)
  SS BOND              : bond        0.00368 (    7)
  SS BOND              : angle       1.07137 (   14)
  hydrogen bonds       : bond        0.02693 (   83)
  hydrogen bonds       : angle       5.55716 (  216)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.148 
Fit side-chains
REVERT: H   73 ASP cc_start: 0.8325 (t70) cc_final: 0.7542 (t0)
REVERT: H   87 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7769 (mtm110)
REVERT: H   91 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8069 (t)
REVERT: H  107 ASP cc_start: 0.8982 (t0) cc_final: 0.8595 (t0)
REVERT: L    5 THR cc_start: 0.9039 (m) cc_final: 0.8659 (p)
REVERT: L   80 GLU cc_start: 0.7463 (mp0) cc_final: 0.7169 (mp0)
REVERT: A  337 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8160 (tm-30)
REVERT: A  386 ASP cc_start: 0.8780 (t0) cc_final: 0.8460 (t0)
REVERT: A  430 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9121 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 73
  average time/residue: 0.1021
  time to fit residues: 8.7441
Evaluate side-chains
  72 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0040
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.7994

-------------------------------------------------------------------------------
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 = 0.3216 r_free = 0.3216 target = 0.086458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.066886 restraints weight = 7598.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 3.67
r_work: 0.2721 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3477  Z= 0.140
  Angle     :  0.625  12.017   4727  Z= 0.313
  Chirality :  0.043   0.128    501
  Planarity :  0.004   0.048    611
  Dihedral  :  4.720  26.500    478
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.71 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 16.89 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.96 (0.39), residues: 425
  helix: -5.28 (0.25), residues: 20
  sheet:  0.10 (0.47), residues: 138
  loop : -1.85 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  46 
 TYR   0.007   0.001   TYR A 505 
 PHE   0.014   0.001   PHE A 389 
 TRP   0.007   0.001   TRP A 350 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3470)
  covalent geometry    : angle       0.62270 ( 4713)
  SS BOND              : bond        0.00375 (    7)
  SS BOND              : angle       1.10088 (   14)
  hydrogen bonds       : bond        0.02707 (   83)
  hydrogen bonds       : angle       5.59868 (  216)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.132 
Fit side-chains
REVERT: H   23 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8078 (ttmm)
REVERT: H   73 ASP cc_start: 0.8320 (t70) cc_final: 0.7534 (t0)
REVERT: H   87 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7777 (mtm110)
REVERT: H   91 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8084 (t)
REVERT: H  107 ASP cc_start: 0.8964 (t0) cc_final: 0.8576 (t0)
REVERT: L    5 THR cc_start: 0.9050 (m) cc_final: 0.8672 (p)
REVERT: L   80 GLU cc_start: 0.7445 (mp0) cc_final: 0.7157 (mp0)
REVERT: A  337 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8174 (tm-30)
REVERT: A  386 ASP cc_start: 0.8766 (t0) cc_final: 0.8437 (t0)
REVERT: A  430 VAL cc_start: 0.9392 (OUTLIER) cc_final: 0.9115 (t)
REVERT: A  513 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7829 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 71
  average time/residue: 0.0852
  time to fit residues: 7.2055
Evaluate side-chains
  73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    0.0970
   chunk 9 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0070
   chunk 32 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.3980
   chunk 37 optimal weight:    2.9990
   chunk 1 optimal weight:    0.3980
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.2996

-------------------------------------------------------------------------------
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 = 0.3258 r_free = 0.3258 target = 0.088881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.069544 restraints weight = 7552.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 3.65
r_work: 0.2780 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   3477  Z= 0.103
  Angle     :  0.613  11.747   4727  Z= 0.300
  Chirality :  0.042   0.123    501
  Planarity :  0.004   0.046    611
  Dihedral  :  4.417  24.894    478
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.29 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 17.71 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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 (0.40), residues: 425
  helix: -5.28 (0.24), residues: 20
  sheet:  0.20 (0.47), residues: 138
  loop : -1.76 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  46 
 TYR   0.016   0.001   TYR H 100 
 PHE   0.013   0.001   PHE A 389 
 TRP   0.007   0.001   TRP A 350 
 HIS   0.000   0.000   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 3470)
  covalent geometry    : angle       0.61247 ( 4713)
  SS BOND              : bond        0.00261 (    7)
  SS BOND              : angle       0.82419 (   14)
  hydrogen bonds       : bond        0.02403 (   83)
  hydrogen bonds       : angle       5.22287 (  216)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.137 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8269 (mt-10)
REVERT: H   73 ASP cc_start: 0.8292 (t70) cc_final: 0.7492 (t0)
REVERT: H   87 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7698 (mtm110)
REVERT: H   91 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7648 (t)
REVERT: H  107 ASP cc_start: 0.8930 (t0) cc_final: 0.8567 (t0)
REVERT: L    5 THR cc_start: 0.9016 (m) cc_final: 0.8686 (p)
REVERT: L   21 LEU cc_start: 0.8979 (mt) cc_final: 0.8690 (mp)
REVERT: L   80 GLU cc_start: 0.7354 (mp0) cc_final: 0.7045 (mp0)
REVERT: A  337 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8157 (tm-30)
REVERT: A  386 ASP cc_start: 0.8704 (t0) cc_final: 0.8420 (t0)
REVERT: A  513 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7761 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0864
  time to fit residues: 8.0007
Evaluate side-chains
  75 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue  366 TYR
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  508 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 13 optimal weight:    4.9990
   chunk 41 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0170
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.5420

-------------------------------------------------------------------------------
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 = 0.3244 r_free = 0.3244 target = 0.088110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.068528 restraints weight = 7511.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 3.69
r_work: 0.2756 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3477  Z= 0.120
  Angle     :  0.621  11.503   4727  Z= 0.308
  Chirality :  0.043   0.126    501
  Planarity :  0.004   0.049    611
  Dihedral  :  4.414  24.483    478
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.76 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 18.53 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.77 (0.40), residues: 425
  helix: -5.27 (0.25), residues: 20
  sheet:  0.26 (0.47), residues: 138
  loop : -1.72 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  18 
 TYR   0.017   0.001   TYR H 100 
 PHE   0.011   0.001   PHE A 389 
 TRP   0.006   0.001   TRP A 350 
 HIS   0.001   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3470)
  covalent geometry    : angle       0.61959 ( 4713)
  SS BOND              : bond        0.00330 (    7)
  SS BOND              : angle       0.94061 (   14)
  hydrogen bonds       : bond        0.02546 (   83)
  hydrogen bonds       : angle       5.24663 (  216)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.133 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8304 (mt-10)
REVERT: H   73 ASP cc_start: 0.8290 (t70) cc_final: 0.7492 (t0)
REVERT: H   87 ARG cc_start: 0.7962 (mtm-85) cc_final: 0.7522 (mtm110)
REVERT: H   91 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7748 (t)
REVERT: H  107 ASP cc_start: 0.8939 (t0) cc_final: 0.8579 (t0)
REVERT: L    5 THR cc_start: 0.9029 (m) cc_final: 0.8703 (p)
REVERT: L   61 ASP cc_start: 0.8795 (p0) cc_final: 0.8521 (t70)
REVERT: A  337 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8166 (tm-30)
REVERT: A  386 ASP cc_start: 0.8726 (t0) cc_final: 0.8434 (t0)
REVERT: A  513 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7761 (tm-30)
  outliers start: 12
  outliers final: 8
  residues processed: 73
  average time/residue: 0.0848
  time to fit residues: 7.3817
Evaluate side-chains
  72 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  508 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3218 r_free = 0.3218 target = 0.086522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.066942 restraints weight = 7545.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 3.70
r_work: 0.2726 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3477  Z= 0.149
  Angle     :  0.640  11.824   4727  Z= 0.319
  Chirality :  0.044   0.135    501
  Planarity :  0.004   0.047    611
  Dihedral  :  4.614  26.183    478
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.24 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.26 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.82 (0.39), residues: 425
  helix: -5.26 (0.26), residues: 20
  sheet:  0.20 (0.47), residues: 138
  loop : -1.75 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  46 
 TYR   0.018   0.001   TYR H 100 
 PHE   0.012   0.001   PHE A 389 
 TRP   0.008   0.001   TRP A 433 
 HIS   0.002   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3470)
  covalent geometry    : angle       0.63767 ( 4713)
  SS BOND              : bond        0.00376 (    7)
  SS BOND              : angle       1.10865 (   14)
  hydrogen bonds       : bond        0.02747 (   83)
  hydrogen bonds       : angle       5.42601 (  216)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.141 
Fit side-chains
REVERT: H   73 ASP cc_start: 0.8309 (t70) cc_final: 0.7499 (t0)
REVERT: H   87 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7924 (mtm110)
REVERT: H   91 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8116 (t)
REVERT: H  107 ASP cc_start: 0.8942 (t0) cc_final: 0.8574 (t0)
REVERT: L    5 THR cc_start: 0.9052 (m) cc_final: 0.8670 (p)
REVERT: L   18 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8067 (ttm-80)
REVERT: L   61 ASP cc_start: 0.8829 (p0) cc_final: 0.8516 (t70)
REVERT: L   80 GLU cc_start: 0.7521 (mp0) cc_final: 0.7263 (mp0)
REVERT: A  337 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8213 (tm-30)
REVERT: A  386 ASP cc_start: 0.8759 (t0) cc_final: 0.8443 (t0)
REVERT: A  430 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9128 (t)
REVERT: A  513 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7766 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 69
  average time/residue: 0.0849
  time to fit residues: 6.9768
Evaluate side-chains
  71 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  508 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    0.0070
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0970
   chunk 21 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0870
   chunk 39 optimal weight:    0.0470
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0980
   overall best weight:    0.0672

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 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 = 0.3296 r_free = 0.3296 target = 0.091235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.071763 restraints weight = 7627.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 3.74
r_work: 0.2823 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   3477  Z= 0.107
  Angle     :  0.615  11.698   4727  Z= 0.303
  Chirality :  0.042   0.126    501
  Planarity :  0.004   0.048    611
  Dihedral  :  4.202  22.939    478
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.88 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.53 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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 (0.40), residues: 425
  helix: -5.24 (0.32), residues: 14
  sheet:  0.06 (0.46), residues: 143
  loop : -1.56 (0.35), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  18 
 TYR   0.017   0.001   TYR H 100 
 PHE   0.009   0.001   PHE A 389 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.001   0.000   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3470)
  covalent geometry    : angle       0.61510 ( 4713)
  SS BOND              : bond        0.00236 (    7)
  SS BOND              : angle       0.69486 (   14)
  hydrogen bonds       : bond        0.02332 (   83)
  hydrogen bonds       : angle       5.06105 (  216)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 934.46 seconds
wall clock time: 16 minutes 41.53 seconds (1001.53 seconds total)