Starting phenix.real_space_refine
on Tue Mar  3 11:32:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qdo_13922/03_2026/7qdo_13922.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qdo_13922/03_2026/7qdo_13922.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qdo_13922/03_2026/7qdo_13922.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qdo_13922/03_2026/7qdo_13922.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qdo_13922/03_2026/7qdo_13922.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qdo_13922/03_2026/7qdo_13922.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.096
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      12      5.16       5
     C    2080      2.51       5
     N     564      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3304
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 1652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1652
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 194}
  Restraints were copied for chains:
    A
  Time building chain proxies: 0.81, per 1000 atoms: 0.25
  Number of scatterers: 3304
  At special positions: 0
  Unit cell: (84.739, 52.857, 80.544, 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      12     16.00
     O     648      8.00
     N     564      7.00
     C    2080      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 367 " - pdb=" SG  CYS B 426 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 474 " - pdb=" SG  CYS B 536 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 367 " - pdb=" SG  CYS A 426 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 536 " distance=2.04

  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: 0.20
  Conformation dependent library (CDL) restraints added in 145.8 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  816

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 12 sheets defined
      11.3% alpha, 38.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'B' and resid 353 through 361
    Processing helix  chain 'B' and resid 414 through 421
      removed outlier: 4.006A  pdb=" N   TRP B 418 " --> pdb=" O   SER B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 530
    Processing helix  chain 'A' and resid 353 through 361
    Processing helix  chain 'A' and resid 414 through 421
      removed outlier: 4.006A  pdb=" N   TRP A 418 " --> pdb=" O   SER A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 530
    Processing sheet with id=AA1, first strand: chain 'B' and resid 346 through 350
      removed outlier: 3.641A  pdb=" N   ARG B 346 " --> pdb=" O   THR B 370 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR B 366 " --> pdb=" O   ILE B 350 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   THR B 363 " --> pdb=" O   ILE B 413 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA B 411 " --> pdb=" O   LEU B 365 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   CYS B 367 " --> pdb=" O   GLY B 409 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLY B 409 " --> pdb=" O   CYS B 367 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 380 through 383
      removed outlier: 3.704A  pdb=" N   VAL B 428 " --> pdb=" O   LEU B 437 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 399 through 400
      removed outlier: 3.966A  pdb=" N   THR B 404 " --> pdb=" O   HIS B 400 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 453 through 457
      removed outlier: 6.202A  pdb=" N   TYR B 515 " --> pdb=" O   GLY B 478 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 453 through 457
      removed outlier: 6.202A  pdb=" N   TYR B 515 " --> pdb=" O   GLY B 478 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 493 through 494
      removed outlier: 3.595A  pdb=" N   CYS B 536 " --> pdb=" O   ARG B 550 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 346 through 350
      removed outlier: 3.641A  pdb=" N   ARG A 346 " --> pdb=" O   THR A 370 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR A 366 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   THR A 363 " --> pdb=" O   ILE A 413 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA A 411 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   CYS A 367 " --> pdb=" O   GLY A 409 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLY A 409 " --> pdb=" O   CYS A 367 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 380 through 383
      removed outlier: 3.705A  pdb=" N   VAL A 428 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 399 through 400
      removed outlier: 3.966A  pdb=" N   THR A 404 " --> pdb=" O   HIS A 400 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 457
      removed outlier: 6.202A  pdb=" N   TYR A 515 " --> pdb=" O   GLY A 478 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 453 through 457
      removed outlier: 6.202A  pdb=" N   TYR A 515 " --> pdb=" O   GLY A 478 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 493 through 494
      removed outlier: 3.595A  pdb=" N   CYS A 536 " --> pdb=" O   ARG A 550 " (cutoff:3.500A)

    136 hydrogen bonds defined for protein.
    348 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.47

  Time building geometry restraints manager: 0.30 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: 1072
        1.34 -     1.46: 706
        1.46 -     1.58: 1596
        1.58 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 3390
  Sorted by residual:
  bond pdb=" N   VAL B 447 "
       pdb=" CA  VAL B 447 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.034 1.27e-02 6.20e+03 7.10e+00
  bond pdb=" N   THR A 533 "
       pdb=" CA  THR A 533 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.032 1.23e-02 6.61e+03 6.89e+00
  bond pdb=" N   THR B 533 "
       pdb=" CA  THR B 533 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.032 1.23e-02 6.61e+03 6.79e+00
  bond pdb=" N   VAL A 447 "
       pdb=" CA  VAL A 447 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.27e-02 6.20e+03 6.76e+00
  bond pdb=" N   SER A 442 "
       pdb=" CA  SER A 442 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.23e-02 6.61e+03 6.64e+00
  ... (remaining 3385 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 4228
        1.29 -     2.58: 321
        2.58 -     3.86: 75
        3.86 -     5.15: 8
        5.15 -     6.44: 12
  Bond angle restraints: 4644
  Sorted by residual:
  angle pdb=" N   ASN A 465 "
        pdb=" CA  ASN A 465 "
        pdb=" C   ASN A 465 "
      ideal   model   delta    sigma   weight residual
     114.56  108.69    5.87 1.27e+00 6.20e-01 2.14e+01
  angle pdb=" N   ASN B 465 "
        pdb=" CA  ASN B 465 "
        pdb=" C   ASN B 465 "
      ideal   model   delta    sigma   weight residual
     114.56  108.69    5.87 1.27e+00 6.20e-01 2.14e+01
  angle pdb=" N   LYS A 445 "
        pdb=" CA  LYS A 445 "
        pdb=" C   LYS A 445 "
      ideal   model   delta    sigma   weight residual
     114.56  110.31    4.25 1.27e+00 6.20e-01 1.12e+01
  angle pdb=" CA  ARG B 491 "
        pdb=" C   ARG B 491 "
        pdb=" O   ARG B 491 "
      ideal   model   delta    sigma   weight residual
     122.03  118.12    3.91 1.17e+00 7.31e-01 1.11e+01
  angle pdb=" N   LYS B 445 "
        pdb=" CA  LYS B 445 "
        pdb=" C   LYS B 445 "
      ideal   model   delta    sigma   weight residual
     114.56  110.33    4.23 1.27e+00 6.20e-01 1.11e+01
  ... (remaining 4639 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.93: 1874
       15.93 -    31.87: 144
       31.87 -    47.80: 36
       47.80 -    63.73: 0
       63.73 -    79.66: 2
  Dihedral angle restraints: 2056
    sinusoidal: 808
      harmonic: 1248
  Sorted by residual:
  dihedral pdb=" CB  CYS A 367 "
           pdb=" SG  CYS A 367 "
           pdb=" SG  CYS A 426 "
           pdb=" CB  CYS A 426 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.29  -44.29     1      1.00e+01 1.00e-02 2.73e+01
  dihedral pdb=" CB  CYS B 367 "
           pdb=" SG  CYS B 367 "
           pdb=" SG  CYS B 426 "
           pdb=" CB  CYS B 426 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.25  -44.25     1      1.00e+01 1.00e-02 2.72e+01
  dihedral pdb=" CB  CYS B 474 "
           pdb=" SG  CYS B 474 "
           pdb=" SG  CYS B 536 "
           pdb=" CB  CYS B 536 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   65.87   27.13     1      1.00e+01 1.00e-02 1.06e+01
  ... (remaining 2053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 344
       0.037 -    0.074: 119
       0.074 -    0.112: 65
       0.112 -    0.149: 14
       0.149 -    0.186: 2
  Chirality restraints: 544
  Sorted by residual:
  chirality pdb=" CA  VAL B 447 "
            pdb=" N   VAL B 447 "
            pdb=" C   VAL B 447 "
            pdb=" CB  VAL B 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.64e-01
  chirality pdb=" CA  VAL A 447 "
            pdb=" N   VAL A 447 "
            pdb=" C   VAL A 447 "
            pdb=" CB  VAL A 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.18 2.00e-01 2.50e+01 8.52e-01
  chirality pdb=" CA  LEU A 449 "
            pdb=" N   LEU A 449 "
            pdb=" C   LEU A 449 "
            pdb=" CB  LEU A 449 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 541 not shown)

  Planarity restraints: 598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 451 "   -0.020 5.00e-02 4.00e+02   3.06e-02 1.50e+00
        pdb=" N   PRO A 452 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 452 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 452 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 451 "   -0.020 5.00e-02 4.00e+02   3.06e-02 1.49e+00
        pdb=" N   PRO B 452 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO B 452 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 452 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 382 "    0.007 2.00e-02 2.50e+03   7.53e-03 1.42e+00
        pdb=" CG  TRP A 382 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 382 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 382 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 382 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 382 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 382 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 382 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 382 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 382 "    0.000 2.00e-02 2.50e+03
  ... (remaining 595 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 401
        2.76 -     3.29: 3134
        3.29 -     3.83: 5189
        3.83 -     4.36: 5766
        4.36 -     4.90: 10067
  Nonbonded interactions: 24557
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 553 "
            pdb=" OG1 THR A 556 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OD1 ASP B 553 "
            pdb=" OG1 THR B 556 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG1 THR B 363 "
            pdb=" O   ILE B 413 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG1 THR A 363 "
            pdb=" O   ILE A 413 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   ASP B 417 "
            pdb=" OG  SER B 420 "
     model   vdw
     2.478 3.040
  ... (remaining 24552 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

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:             1.840
  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:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.570
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
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      :  0.005   0.037   3394  Z= 0.318
  Angle     :  0.824   6.438   4652  Z= 0.510
  Chirality :  0.049   0.186    544
  Planarity :  0.005   0.031    598
  Dihedral  : 11.618  79.664   1228
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.40), residues: 420
  helix: -0.82 (0.83), residues: 44
  sheet:  1.32 (0.37), residues: 180
  loop : -2.45 (0.40), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 514 
 TYR   0.011   0.002   TYR A 500 
 PHE   0.013   0.003   PHE A 479 
 TRP   0.020   0.002   TRP A 382 
 HIS   0.004   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 3390)
  covalent geometry    : angle       0.82287 ( 4644)
  SS BOND              : bond        0.00840 (    4)
  SS BOND              : angle       1.36010 (    8)
  hydrogen bonds       : bond        0.25403 (  106)
  hydrogen bonds       : angle       9.34136 (  348)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0684
  time to fit residues: 8.0255
Evaluate side-chains
  67 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0040
   chunk 32 optimal weight:    0.0980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    0.3980
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.3150

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

Flipped N/Q/H residues before XYZ refinement:
** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 439 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 = 0.4370 r_free = 0.4370 target = 0.189690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.139628 restraints weight = 5243.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.144626 restraints weight = 2889.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.147888 restraints weight = 2025.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.149667 restraints weight = 1638.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.150912 restraints weight = 1447.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3394  Z= 0.131
  Angle     :  0.668   5.754   4652  Z= 0.353
  Chirality :  0.046   0.162    544
  Planarity :  0.005   0.039    598
  Dihedral  :  4.149  15.463    454
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.58 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.40), residues: 420
  helix: -0.41 (0.74), residues: 44
  sheet:  1.37 (0.39), residues: 174
  loop : -1.77 (0.40), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 491 
 TYR   0.003   0.001   TYR A 500 
 PHE   0.010   0.002   PHE B 516 
 TRP   0.005   0.001   TRP B 382 
 HIS   0.008   0.001   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3390)
  covalent geometry    : angle       0.66768 ( 4644)
  SS BOND              : bond        0.00901 (    4)
  SS BOND              : angle       1.02803 (    8)
  hydrogen bonds       : bond        0.05062 (  106)
  hydrogen bonds       : angle       6.25832 (  348)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  506 MET cc_start: 0.6553 (mmm) cc_final: 0.5877 (ptt)
REVERT: A  506 MET cc_start: 0.6626 (mmm) cc_final: 0.5970 (ptt)
  outliers start: 4
  outliers final: 4
  residues processed: 81
  average time/residue: 0.0699
  time to fit residues: 6.8132
Evaluate side-chains
  61 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  445 LYS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  445 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 439 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 = 0.4330 r_free = 0.4330 target = 0.185674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.134645 restraints weight = 5244.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.139711 restraints weight = 2992.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.142793 restraints weight = 2128.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.144814 restraints weight = 1729.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.145922 restraints weight = 1520.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3394  Z= 0.147
  Angle     :  0.648   5.855   4652  Z= 0.339
  Chirality :  0.045   0.152    544
  Planarity :  0.004   0.028    598
  Dihedral  :  4.185  15.576    454
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 13.49 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.40), residues: 420
  helix: -0.32 (0.76), residues: 44
  sheet:  1.46 (0.40), residues: 160
  loop : -1.76 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 467 
 TYR   0.016   0.002   TYR A 500 
 PHE   0.019   0.002   PHE B 479 
 TRP   0.009   0.001   TRP A 528 
 HIS   0.006   0.001   HIS B 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3390)
  covalent geometry    : angle       0.64495 ( 4644)
  SS BOND              : bond        0.00956 (    4)
  SS BOND              : angle       1.53098 (    8)
  hydrogen bonds       : bond        0.04590 (  106)
  hydrogen bonds       : angle       5.64842 (  348)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  506 MET cc_start: 0.6825 (mmm) cc_final: 0.5810 (ptp)
REVERT: A  506 MET cc_start: 0.6782 (mmm) cc_final: 0.5968 (ptt)
  outliers start: 13
  outliers final: 8
  residues processed: 69
  average time/residue: 0.0710
  time to fit residues: 5.8405
Evaluate side-chains
  61 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  445 LYS
Chi-restraints excluded: chain B residue  545 ASN
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  445 LYS
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  545 ASN
Chi-restraints excluded: chain A residue  547 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 26 optimal weight:    9.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 518 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.185365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.134168 restraints weight = 5171.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.139167 restraints weight = 2962.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.142225 restraints weight = 2116.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.143971 restraints weight = 1722.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.145182 restraints weight = 1524.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3394  Z= 0.139
  Angle     :  0.650   6.273   4652  Z= 0.338
  Chirality :  0.044   0.149    544
  Planarity :  0.004   0.030    598
  Dihedral  :  4.163  15.537    454
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.25 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.40), residues: 420
  helix: -0.68 (0.74), residues: 44
  sheet:  1.37 (0.39), residues: 160
  loop : -1.75 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 491 
 TYR   0.017   0.002   TYR A 500 
 PHE   0.015   0.002   PHE A 479 
 TRP   0.010   0.001   TRP A 528 
 HIS   0.005   0.001   HIS B 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3390)
  covalent geometry    : angle       0.64723 ( 4644)
  SS BOND              : bond        0.00967 (    4)
  SS BOND              : angle       1.65217 (    8)
  hydrogen bonds       : bond        0.04141 (  106)
  hydrogen bonds       : angle       5.38891 (  348)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  489 MET cc_start: 0.8042 (tpp) cc_final: 0.7281 (mmm)
REVERT: B  506 MET cc_start: 0.6852 (mmm) cc_final: 0.5930 (ptp)
REVERT: A  489 MET cc_start: 0.8030 (tpp) cc_final: 0.7282 (mmm)
REVERT: A  506 MET cc_start: 0.6802 (mmm) cc_final: 0.5913 (ptp)
  outliers start: 11
  outliers final: 6
  residues processed: 68
  average time/residue: 0.0889
  time to fit residues: 7.0604
Evaluate side-chains
  61 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  518 HIS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  445 LYS
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  547 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    0.1980
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 6 optimal weight:    0.2980
   chunk 1 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0870
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
A 439 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.186880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.135845 restraints weight = 5223.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.140781 restraints weight = 3041.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.143968 restraints weight = 2177.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.145856 restraints weight = 1774.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.147000 restraints weight = 1565.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3394  Z= 0.117
  Angle     :  0.655   5.897   4652  Z= 0.338
  Chirality :  0.045   0.201    544
  Planarity :  0.004   0.029    598
  Dihedral  :  4.100  15.603    454
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.63 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.40), residues: 420
  helix: -0.90 (0.75), residues: 44
  sheet:  1.43 (0.39), residues: 160
  loop : -1.74 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 491 
 TYR   0.015   0.001   TYR A 500 
 PHE   0.009   0.002   PHE B 479 
 TRP   0.009   0.001   TRP B 528 
 HIS   0.004   0.001   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 3390)
  covalent geometry    : angle       0.65370 ( 4644)
  SS BOND              : bond        0.00785 (    4)
  SS BOND              : angle       1.33375 (    8)
  hydrogen bonds       : bond        0.03907 (  106)
  hydrogen bonds       : angle       4.98991 (  348)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  489 MET cc_start: 0.8061 (tpp) cc_final: 0.7276 (mmm)
REVERT: A  489 MET cc_start: 0.8035 (tpp) cc_final: 0.7252 (mmm)
REVERT: A  506 MET cc_start: 0.6739 (mmm) cc_final: 0.5518 (mtm)
  outliers start: 9
  outliers final: 5
  residues processed: 70
  average time/residue: 0.0867
  time to fit residues: 7.0730
Evaluate side-chains
  65 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  445 LYS
Chi-restraints excluded: chain B residue  518 HIS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  445 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 518 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.183379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.132489 restraints weight = 5238.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.137308 restraints weight = 3025.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.140330 restraints weight = 2167.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.142292 restraints weight = 1768.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.143388 restraints weight = 1562.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3394  Z= 0.151
  Angle     :  0.690   9.179   4652  Z= 0.354
  Chirality :  0.046   0.187    544
  Planarity :  0.004   0.030    598
  Dihedral  :  4.368  15.749    454
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.22 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.41), residues: 420
  helix: -0.68 (0.80), residues: 44
  sheet:  1.54 (0.40), residues: 160
  loop : -1.77 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 461 
 TYR   0.010   0.001   TYR B 500 
 PHE   0.019   0.002   PHE B 405 
 TRP   0.011   0.001   TRP B 382 
 HIS   0.005   0.001   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3390)
  covalent geometry    : angle       0.68644 ( 4644)
  SS BOND              : bond        0.01134 (    4)
  SS BOND              : angle       1.72501 (    8)
  hydrogen bonds       : bond        0.04057 (  106)
  hydrogen bonds       : angle       5.00695 (  348)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  439 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7654 (mp10)
REVERT: B  506 MET cc_start: 0.6593 (mmm) cc_final: 0.5550 (mtm)
REVERT: A  506 MET cc_start: 0.6898 (mmm) cc_final: 0.5631 (mtm)
  outliers start: 11
  outliers final: 6
  residues processed: 64
  average time/residue: 0.0764
  time to fit residues: 5.8433
Evaluate side-chains
  64 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  445 LYS
Chi-restraints excluded: chain B residue  518 HIS
Chi-restraints excluded: chain B residue  545 ASN
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  545 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0040
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.1398

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

Flipped N/Q/H residues before XYZ refinement:
** B 518 HIS ** 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 = 0.4277 r_free = 0.4277 target = 0.180992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.130007 restraints weight = 5258.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.134760 restraints weight = 3016.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.137814 restraints weight = 2160.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.139610 restraints weight = 1763.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.140789 restraints weight = 1560.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3394  Z= 0.168
  Angle     :  0.684   6.604   4652  Z= 0.354
  Chirality :  0.046   0.196    544
  Planarity :  0.004   0.034    598
  Dihedral  :  4.447  17.720    454
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 21.96 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.41), residues: 420
  helix: -0.58 (0.82), residues: 44
  sheet:  1.55 (0.40), residues: 160
  loop : -1.75 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 514 
 TYR   0.009   0.001   TYR B 500 
 PHE   0.020   0.003   PHE B 479 
 TRP   0.014   0.002   TRP B 382 
 HIS   0.004   0.001   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 3390)
  covalent geometry    : angle       0.67978 ( 4644)
  SS BOND              : bond        0.01193 (    4)
  SS BOND              : angle       1.99856 (    8)
  hydrogen bonds       : bond        0.04123 (  106)
  hydrogen bonds       : angle       5.06835 (  348)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  439 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7597 (mp10)
REVERT: B  489 MET cc_start: 0.8096 (tpp) cc_final: 0.7365 (mmm)
REVERT: B  506 MET cc_start: 0.6704 (mmm) cc_final: 0.5534 (mtm)
  outliers start: 12
  outliers final: 8
  residues processed: 69
  average time/residue: 0.0602
  time to fit residues: 5.2856
Evaluate side-chains
  70 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  445 LYS
Chi-restraints excluded: chain B residue  518 HIS
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  545 ASN
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  545 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 518 HIS ** 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 = 0.4271 r_free = 0.4271 target = 0.180308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.129132 restraints weight = 5245.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.133892 restraints weight = 3023.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.136960 restraints weight = 2172.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.138710 restraints weight = 1772.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.139598 restraints weight = 1570.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3394  Z= 0.166
  Angle     :  0.719  10.632   4652  Z= 0.369
  Chirality :  0.046   0.164    544
  Planarity :  0.004   0.034    598
  Dihedral  :  4.579  17.803    454
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 22.22 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.41), residues: 420
  helix: -0.65 (0.81), residues: 44
  sheet:  1.49 (0.40), residues: 160
  loop : -1.80 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 467 
 TYR   0.007   0.001   TYR A 455 
 PHE   0.018   0.002   PHE A 479 
 TRP   0.021   0.002   TRP B 382 
 HIS   0.004   0.001   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 3390)
  covalent geometry    : angle       0.71593 ( 4644)
  SS BOND              : bond        0.01047 (    4)
  SS BOND              : angle       1.79787 (    8)
  hydrogen bonds       : bond        0.04197 (  106)
  hydrogen bonds       : angle       4.99169 (  348)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  506 MET cc_start: 0.6639 (mmm) cc_final: 0.5569 (mtm)
REVERT: A  506 MET cc_start: 0.6650 (mmm) cc_final: 0.5586 (mtm)
  outliers start: 9
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0592
  time to fit residues: 4.9264
Evaluate side-chains
  66 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  518 HIS
Chi-restraints excluded: chain B residue  545 ASN
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  545 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 439 GLN
** A 518 HIS ** 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 = 0.4263 r_free = 0.4263 target = 0.179452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.129440 restraints weight = 5182.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.134256 restraints weight = 2918.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.137266 restraints weight = 2065.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.139127 restraints weight = 1670.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.140312 restraints weight = 1466.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3394  Z= 0.156
  Angle     :  0.719   7.666   4652  Z= 0.370
  Chirality :  0.046   0.153    544
  Planarity :  0.004   0.034    598
  Dihedral  :  4.560  18.232    454
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 22.22 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.41), residues: 420
  helix: -0.70 (0.79), residues: 44
  sheet:  1.52 (0.41), residues: 160
  loop : -1.80 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 467 
 TYR   0.011   0.001   TYR B 500 
 PHE   0.015   0.002   PHE B 479 
 TRP   0.022   0.002   TRP B 382 
 HIS   0.004   0.001   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3390)
  covalent geometry    : angle       0.71572 ( 4644)
  SS BOND              : bond        0.01033 (    4)
  SS BOND              : angle       1.74696 (    8)
  hydrogen bonds       : bond        0.04128 (  106)
  hydrogen bonds       : angle       4.89495 (  348)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  506 MET cc_start: 0.6638 (mmm) cc_final: 0.5554 (mtm)
REVERT: A  506 MET cc_start: 0.6721 (mmm) cc_final: 0.5684 (mtm)
  outliers start: 10
  outliers final: 7
  residues processed: 66
  average time/residue: 0.0603
  time to fit residues: 4.8837
Evaluate side-chains
  66 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  518 HIS
Chi-restraints excluded: chain B residue  545 ASN
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  545 ASN
Chi-restraints excluded: chain A residue  547 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0070
   chunk 7 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0020
   chunk 30 optimal weight:    0.0170
   chunk 40 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.3044

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

Flipped N/Q/H residues before XYZ refinement:
B 518 HIS
A 439 GLN
A 518 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.182400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.132900 restraints weight = 5153.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.137613 restraints weight = 2947.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.140617 restraints weight = 2085.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.142365 restraints weight = 1686.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.143574 restraints weight = 1478.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.4250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3394  Z= 0.130
  Angle     :  0.695   6.047   4652  Z= 0.359
  Chirality :  0.045   0.146    544
  Planarity :  0.004   0.035    598
  Dihedral  :  4.528  18.789    454
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.48 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 24.34 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.41), residues: 420
  helix: -1.00 (0.73), residues: 44
  sheet:  1.50 (0.40), residues: 160
  loop : -1.76 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 467 
 TYR   0.016   0.001   TYR B 500 
 PHE   0.010   0.002   PHE B 405 
 TRP   0.028   0.002   TRP A 382 
 HIS   0.005   0.001   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3390)
  covalent geometry    : angle       0.69420 ( 4644)
  SS BOND              : bond        0.00801 (    4)
  SS BOND              : angle       1.18222 (    8)
  hydrogen bonds       : bond        0.04032 (  106)
  hydrogen bonds       : angle       4.80288 (  348)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  439 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7584 (mp10)
REVERT: B  506 MET cc_start: 0.6590 (mmm) cc_final: 0.5513 (mtm)
REVERT: A  438 LYS cc_start: 0.8846 (mmtp) cc_final: 0.8587 (mmtt)
REVERT: A  506 MET cc_start: 0.6590 (mmm) cc_final: 0.5636 (mtm)
  outliers start: 4
  outliers final: 4
  residues processed: 63
  average time/residue: 0.0567
  time to fit residues: 4.4766
Evaluate side-chains
  62 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  518 HIS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  547 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0270
   chunk 2 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
** B 518 HIS ** 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 = 0.4278 r_free = 0.4278 target = 0.181171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.131408 restraints weight = 5268.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.136125 restraints weight = 2969.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.139040 restraints weight = 2101.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.140918 restraints weight = 1700.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.142033 restraints weight = 1492.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.4372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3394  Z= 0.135
  Angle     :  0.687   5.596   4652  Z= 0.357
  Chirality :  0.045   0.147    544
  Planarity :  0.004   0.033    598
  Dihedral  :  4.465  19.934    454
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 23.81 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.41), residues: 420
  helix: -0.91 (0.74), residues: 44
  sheet:  1.45 (0.40), residues: 160
  loop : -1.71 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 491 
 TYR   0.021   0.001   TYR B 500 
 PHE   0.012   0.002   PHE B 479 
 TRP   0.033   0.003   TRP A 382 
 HIS   0.002   0.001   HIS A 393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 3390)
  covalent geometry    : angle       0.68391 ( 4644)
  SS BOND              : bond        0.01021 (    4)
  SS BOND              : angle       1.61794 (    8)
  hydrogen bonds       : bond        0.04059 (  106)
  hydrogen bonds       : angle       4.77164 (  348)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 857.18 seconds
wall clock time: 15 minutes 19.56 seconds (919.56 seconds total)