Starting phenix.real_space_refine
on Mon Feb 10 23:59:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qdo_13922/02_2025/7qdo_13922.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qdo_13922/02_2025/7qdo_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_13922/02_2025/7qdo_13922.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qdo_13922/02_2025/7qdo_13922.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qdo_13922/02_2025/7qdo_13922.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qdo_13922/02_2025/7qdo_13922.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3304
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      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:
    B
  Time building chain proxies: 2.87, per 1000 atoms: 0.87
  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=2, 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

  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: 0.66
  Conformation dependent library (CDL) restraints added in 323.1 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: 0.43
  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: 0.86

  Time building geometry restraints manager: 0.78 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: 1872
       15.93 -    31.87: 142
       31.87 -    47.80: 34
       47.80 -    63.73: 0
       63.73 -    79.66: 2
  Dihedral angle restraints: 2050
    sinusoidal: 802
      harmonic: 1248
  Sorted by residual:
  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
  dihedral pdb=" CA  MET B 506 "
           pdb=" C   MET B 506 "
           pdb=" N   PRO B 507 "
           pdb=" CA  PRO B 507 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.98  -16.02     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 2047 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:
        2.04 -     2.61: 28
        2.61 -     3.18: 2840
        3.18 -     3.76: 4774
        3.76 -     4.33: 6386
        4.33 -     4.90: 10535
  Nonbonded interactions: 24563
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A 367 "
            pdb=" SG  CYS A 426 "
     model   vdw
     2.038 3.760
  nonbonded pdb=" SG  CYS A 474 "
            pdb=" SG  CYS A 536 "
     model   vdw
     2.041 3.760
  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
  ... (remaining 24558 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.730
  Find NCS groups from input model:        0.060
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.910
-------------------------------------------------------------------------------
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   3390  Z= 0.337
  Angle     :  0.823   6.438   4644  Z= 0.510
  Chirality :  0.049   0.186    544
  Planarity :  0.005   0.031    598
  Dihedral  : 11.618  79.664   1228
  Min Nonbonded Distance : 2.038

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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.020   0.002   TRP A 382 
 HIS   0.004   0.001   HIS A 540 
 PHE   0.013   0.003   PHE A 479 
 TYR   0.011   0.002   TYR A 500 
 ARG   0.004   0.001   ARG A 514 

*********************** 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  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1737
  time to fit residues: 19.9699
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  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 21 optimal weight:    4.9990
   chunk 32 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   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 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.185515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.135747 restraints weight = 5153.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.140581 restraints weight = 2869.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.143703 restraints weight = 2034.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3390  Z= 0.220
  Angle     :  0.675   6.228   4644  Z= 0.358
  Chirality :  0.047   0.161    544
  Planarity :  0.005   0.036    598
  Dihedral  :  4.230  16.473    454
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 10.58 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.41), residues: 420
  helix: -0.36 (0.74), residues: 44
  sheet:  1.34 (0.40), residues: 174
  loop : -1.77 (0.40), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 488 
 HIS   0.007   0.001   HIS A 518 
 PHE   0.017   0.002   PHE A 479 
 TYR   0.005   0.001   TYR A 534 
 ARG   0.004   0.000   ARG A 491 

*********************** 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
  89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  417 ASP cc_start: 0.8468 (p0) cc_final: 0.8155 (p0)
REVERT: B  506 MET cc_start: 0.6700 (mmm) cc_final: 0.6004 (ptt)
REVERT: A  367 CYS cc_start: 0.7609 (p) cc_final: 0.7219 (p)
REVERT: A  417 ASP cc_start: 0.8403 (p0) cc_final: 0.8169 (p0)
REVERT: A  506 MET cc_start: 0.6738 (mmm) cc_final: 0.5997 (ptt)
  outliers start: 7
  outliers final: 6
  residues processed: 84
  average time/residue: 0.1709
  time to fit residues: 17.2296
Evaluate side-chains
  62 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
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  545 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0020
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.5988

-------------------------------------------------------------------------------
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 = 0.4335 r_free = 0.4335 target = 0.185881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.135142 restraints weight = 5166.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.140063 restraints weight = 3025.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.143128 restraints weight = 2171.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3390  Z= 0.183
  Angle     :  0.621   5.911   4644  Z= 0.325
  Chirality :  0.044   0.152    544
  Planarity :  0.004   0.031    598
  Dihedral  :  4.134  15.268    454
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 14.55 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.40), residues: 420
  helix: -0.43 (0.75), residues: 44
  sheet:  1.39 (0.40), residues: 160
  loop : -1.79 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 528 
 HIS   0.006   0.001   HIS B 518 
 PHE   0.013   0.002   PHE B 479 
 TYR   0.016   0.001   TYR A 500 
 ARG   0.003   0.000   ARG A 467 

*********************** 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
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.395 
Fit side-chains
REVERT: B  438 LYS cc_start: 0.8754 (mttt) cc_final: 0.8290 (mmtt)
REVERT: B  506 MET cc_start: 0.6808 (mmm) cc_final: 0.5769 (ptp)
REVERT: A  367 CYS cc_start: 0.7693 (p) cc_final: 0.7190 (p)
REVERT: A  489 MET cc_start: 0.8009 (tpp) cc_final: 0.7185 (mmm)
REVERT: A  506 MET cc_start: 0.6775 (mmm) cc_final: 0.5944 (ptt)
  outliers start: 12
  outliers final: 6
  residues processed: 73
  average time/residue: 0.1817
  time to fit residues: 15.9390
Evaluate side-chains
  60 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 34 optimal weight:    0.2980
   chunk 26 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0370
   overall best weight:    1.6664

-------------------------------------------------------------------------------
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 = 0.4252 r_free = 0.4252 target = 0.177450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.126636 restraints weight = 5118.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.131082 restraints weight = 3074.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.133881 restraints weight = 2253.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3390  Z= 0.356
  Angle     :  0.757   7.372   4644  Z= 0.398
  Chirality :  0.047   0.146    544
  Planarity :  0.005   0.032    598
  Dihedral  :  4.729  17.842    454
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 18.25 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.42), residues: 420
  helix: -0.48 (0.80), residues: 44
  sheet:  1.39 (0.41), residues: 160
  loop : -1.85 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 528 
 HIS   0.006   0.002   HIS A 393 
 PHE   0.024   0.004   PHE A 479 
 TYR   0.019   0.003   TYR A 500 
 ARG   0.003   0.001   ARG B 491 

*********************** 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
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: B  441 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8871 (mm)
REVERT: B  489 MET cc_start: 0.8029 (tpp) cc_final: 0.7784 (mtp)
REVERT: A  367 CYS cc_start: 0.7738 (p) cc_final: 0.7332 (p)
  outliers start: 16
  outliers final: 8
  residues processed: 72
  average time/residue: 0.2081
  time to fit residues: 17.9759
Evaluate side-chains
  72 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  441 ILE
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  445 LYS
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  545 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    0.1980
   chunk 16 optimal weight:    0.0370
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 = 0.4287 r_free = 0.4287 target = 0.181569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.130495 restraints weight = 5129.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.135527 restraints weight = 2909.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.138614 restraints weight = 2066.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3390  Z= 0.190
  Angle     :  0.683   8.039   4644  Z= 0.347
  Chirality :  0.045   0.146    544
  Planarity :  0.005   0.036    598
  Dihedral  :  4.457  16.741    454
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.05 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.41), residues: 420
  helix: -0.73 (0.77), residues: 44
  sheet:  1.44 (0.41), residues: 160
  loop : -1.85 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 528 
 HIS   0.005   0.001   HIS B 518 
 PHE   0.010   0.002   PHE A 479 
 TYR   0.016   0.001   TYR A 500 
 ARG   0.006   0.000   ARG A 491 

*********************** 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
  82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.361 
Fit side-chains
REVERT: B  350 ILE cc_start: 0.9114 (mp) cc_final: 0.8832 (tp)
REVERT: B  441 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8867 (mm)
REVERT: B  506 MET cc_start: 0.6765 (mmm) cc_final: 0.5557 (mtm)
REVERT: A  367 CYS cc_start: 0.7708 (p) cc_final: 0.6985 (p)
REVERT: A  506 MET cc_start: 0.6810 (mmm) cc_final: 0.5580 (mtm)
  outliers start: 11
  outliers final: 6
  residues processed: 73
  average time/residue: 0.2079
  time to fit residues: 17.8298
Evaluate side-chains
  69 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  441 ILE
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  518 HIS
Chi-restraints excluded: chain A residue  545 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0570
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0870
   overall best weight:    0.7478

-------------------------------------------------------------------------------
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 = 0.4257 r_free = 0.4257 target = 0.178825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.128034 restraints weight = 5266.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.132634 restraints weight = 2976.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.135635 restraints weight = 2121.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3390  Z= 0.207
  Angle     :  0.672   6.272   4644  Z= 0.346
  Chirality :  0.045   0.146    544
  Planarity :  0.004   0.033    598
  Dihedral  :  4.409  16.978    454
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.37 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.41), residues: 420
  helix: -1.02 (0.76), residues: 44
  sheet:  1.57 (0.41), residues: 160
  loop : -1.84 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 382 
 HIS   0.004   0.001   HIS A 518 
 PHE   0.014   0.002   PHE A 479 
 TYR   0.014   0.001   TYR A 500 
 ARG   0.004   0.000   ARG B 491 

*********************** 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
  79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.403 
Fit side-chains
REVERT: B  350 ILE cc_start: 0.9103 (mp) cc_final: 0.8831 (tp)
REVERT: B  438 LYS cc_start: 0.8181 (mmtp) cc_final: 0.7941 (mmtt)
REVERT: B  441 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8884 (mm)
REVERT: B  468 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7678 (pt0)
REVERT: B  506 MET cc_start: 0.6856 (mmm) cc_final: 0.5555 (mtm)
REVERT: A  367 CYS cc_start: 0.7773 (p) cc_final: 0.7072 (p)
REVERT: A  506 MET cc_start: 0.6910 (mmm) cc_final: 0.5667 (mtm)
  outliers start: 13
  outliers final: 8
  residues processed: 70
  average time/residue: 0.1987
  time to fit residues: 16.6286
Evaluate side-chains
  69 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  445 LYS
Chi-restraints excluded: chain B residue  489 MET
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0570
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 13 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.4275 r_free = 0.4275 target = 0.180265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.129496 restraints weight = 5165.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.134103 restraints weight = 2917.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.137137 restraints weight = 2079.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3390  Z= 0.187
  Angle     :  0.642   5.739   4644  Z= 0.331
  Chirality :  0.045   0.170    544
  Planarity :  0.004   0.034    598
  Dihedral  :  4.287  16.157    454
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.11 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.41), residues: 420
  helix: -1.13 (0.73), residues: 44
  sheet:  1.68 (0.41), residues: 160
  loop : -1.80 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 382 
 HIS   0.004   0.001   HIS A 518 
 PHE   0.011   0.002   PHE A 479 
 TYR   0.012   0.001   TYR B 500 
 ARG   0.003   0.000   ARG A 467 

*********************** 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
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.349 
Fit side-chains
REVERT: B  350 ILE cc_start: 0.9099 (mp) cc_final: 0.8839 (pt)
REVERT: B  438 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7821 (mmtt)
REVERT: B  441 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8858 (mm)
REVERT: B  468 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7620 (pt0)
REVERT: A  506 MET cc_start: 0.6853 (mmm) cc_final: 0.5678 (mtm)
REVERT: A  536 CYS cc_start: 0.8661 (p) cc_final: 0.8298 (t)
  outliers start: 13
  outliers final: 6
  residues processed: 71
  average time/residue: 0.1725
  time to fit residues: 14.6732
Evaluate side-chains
  69 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  489 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0170
   chunk 31 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0030
   chunk 1 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    0.6830

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.179401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.129375 restraints weight = 5152.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.134063 restraints weight = 2865.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.137038 restraints weight = 2026.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.4318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3390  Z= 0.211
  Angle     :  0.697  14.190   4644  Z= 0.350
  Chirality :  0.045   0.145    544
  Planarity :  0.004   0.032    598
  Dihedral  :  4.320  16.949    454
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 21.16 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.41), residues: 420
  helix: -1.27 (0.71), residues: 44
  sheet:  1.67 (0.41), residues: 160
  loop : -1.81 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 382 
 HIS   0.006   0.001   HIS A 518 
 PHE   0.013   0.002   PHE B 479 
 TYR   0.012   0.001   TYR B 500 
 ARG   0.002   0.000   ARG B 491 

*********************** 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
  74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.392 
Fit side-chains
REVERT: B  350 ILE cc_start: 0.9089 (mp) cc_final: 0.8810 (pt)
REVERT: B  438 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7857 (mmtt)
REVERT: B  441 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8789 (mm)
REVERT: B  506 MET cc_start: 0.6403 (mmm) cc_final: 0.5303 (mtm)
REVERT: A  506 MET cc_start: 0.6919 (mmm) cc_final: 0.5718 (mtm)
  outliers start: 11
  outliers final: 9
  residues processed: 68
  average time/residue: 0.1416
  time to fit residues: 12.1974
Evaluate side-chains
  68 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  489 MET
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  350 ILE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  545 ASN
Chi-restraints excluded: chain A residue  547 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 28 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 14 optimal weight:    0.2980
   chunk 6 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4262 r_free = 0.4262 target = 0.179298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.128849 restraints weight = 5220.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.133366 restraints weight = 3028.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.136136 restraints weight = 2195.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.4429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3390  Z= 0.200
  Angle     :  0.680  11.627   4644  Z= 0.344
  Chirality :  0.045   0.145    544
  Planarity :  0.004   0.033    598
  Dihedral  :  4.342  16.912    454
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 22.49 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.41), residues: 420
  helix: -1.29 (0.72), residues: 44
  sheet:  1.69 (0.41), residues: 160
  loop : -1.74 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 382 
 HIS   0.005   0.001   HIS B 518 
 PHE   0.013   0.002   PHE A 479 
 TYR   0.012   0.001   TYR B 500 
 ARG   0.002   0.000   ARG B 491 

*********************** 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
  67 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.289 
Fit side-chains
REVERT: B  350 ILE cc_start: 0.9075 (mp) cc_final: 0.8819 (pt)
REVERT: B  438 LYS cc_start: 0.8045 (mmtp) cc_final: 0.7798 (mmtt)
REVERT: B  441 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8754 (mm)
REVERT: B  467 ARG cc_start: 0.7817 (mmt180) cc_final: 0.7468 (mpt-90)
REVERT: B  506 MET cc_start: 0.6321 (mmm) cc_final: 0.5385 (mtm)
REVERT: A  506 MET cc_start: 0.6815 (mmm) cc_final: 0.5705 (mtm)
  outliers start: 8
  outliers final: 7
  residues processed: 64
  average time/residue: 0.1244
  time to fit residues: 10.4417
Evaluate side-chains
  64 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain B residue  545 ASN
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  363 THR
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 23 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0470
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0970
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 14 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.4276

-------------------------------------------------------------------------------
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 = 0.4274 r_free = 0.4274 target = 0.180588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.130831 restraints weight = 5082.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.135158 restraints weight = 2936.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.138011 restraints weight = 2127.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.4539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3390  Z= 0.180
  Angle     :  0.671  10.367   4644  Z= 0.341
  Chirality :  0.045   0.145    544
  Planarity :  0.004   0.033    598
  Dihedral  :  4.341  18.379    454
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 22.49 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.42), residues: 420
  helix: -1.35 (0.70), residues: 44
  sheet:  1.80 (0.41), residues: 160
  loop : -1.68 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP A 382 
 HIS   0.007   0.001   HIS B 518 
 PHE   0.014   0.002   PHE A 405 
 TYR   0.017   0.001   TYR B 500 
 ARG   0.002   0.000   ARG A 491 

********************** 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
  67 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.391 
Fit side-chains
REVERT: B  350 ILE cc_start: 0.9086 (mp) cc_final: 0.8822 (tp)
REVERT: B  382 TRP cc_start: 0.7085 (m100) cc_final: 0.6526 (m-10)
REVERT: B  438 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7768 (mmtt)
REVERT: B  441 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8761 (mm)
REVERT: B  467 ARG cc_start: 0.7812 (mmt180) cc_final: 0.7466 (mpt-90)
REVERT: B  506 MET cc_start: 0.6323 (mmm) cc_final: 0.5340 (mtm)
REVERT: A  506 MET cc_start: 0.6825 (mmm) cc_final: 0.5716 (mtm)
  outliers start: 9
  outliers final: 6
  residues processed: 63
  average time/residue: 0.1243
  time to fit residues: 10.0280
Evaluate side-chains
  62 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  363 THR
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 1 optimal weight:    0.0670
   chunk 32 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 4 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.5320

-------------------------------------------------------------------------------
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 = 0.4263 r_free = 0.4263 target = 0.179803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.130125 restraints weight = 5155.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.134508 restraints weight = 2956.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.137255 restraints weight = 2124.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3390  Z= 0.198
  Angle     :  0.683   9.811   4644  Z= 0.349
  Chirality :  0.045   0.147    544
  Planarity :  0.004   0.033    598
  Dihedral  :  4.349  19.646    454
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 22.49 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.42), residues: 420
  helix: -1.50 (0.68), residues: 46
  sheet:  1.86 (0.41), residues: 160
  loop : -1.67 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 382 
 HIS   0.006   0.001   HIS B 518 
 PHE   0.011   0.002   PHE A 479 
 TYR   0.020   0.001   TYR B 500 
 ARG   0.003   0.000   ARG B 491 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1508.23 seconds
wall clock time: 27 minutes 58.07 seconds (1678.07 seconds total)