Starting phenix.real_space_refine
on Thu Jun  5 07:27:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.cif"
  }
  resolution = 3.86
  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=   0.018 sd=   0.094
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      60      5.16       5
     C    3682      2.51       5
     N     834      2.21       5
     O     852      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5428
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2679
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 8, 'TRANS': 324}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 2679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2679
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 8, 'TRANS': 324}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 35
          Unusual residues: {'CHT': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 35
          Unusual residues: {'CHT': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.05, per 1000 atoms: 0.75
  Number of scatterers: 5428
  At special positions: 0
  Unit cell: (107.613, 120.657, 82.612, 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      60     16.00
     O     852      8.00
     N     834      7.00
     C    3682      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.32
  Conformation dependent library (CDL) restraints added in 647.8 milliseconds
  

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1276

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      83.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 51
    Processing helix  chain 'A' and resid 228 through 245
      removed outlier: 5.997A  pdb=" N   ARG A 234 " --> pdb=" O   MET A 230 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   TYR A 235 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ARG A 238 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 309
    Processing helix  chain 'A' and resid 310 through 331
    Processing helix  chain 'A' and resid 333 through 336
    Processing helix  chain 'A' and resid 337 through 356
      removed outlier: 3.515A  pdb=" N   THR A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 416
      removed outlier: 3.614A  pdb=" N   ILE A 393 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 430
    Processing helix  chain 'A' and resid 431 through 438
    Processing helix  chain 'A' and resid 439 through 466
      removed outlier: 3.545A  pdb=" N   VAL A 443 " --> pdb=" O   HIS A 439 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL A 453 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
      Proline residue:  A 456  - end of helix
    Processing helix  chain 'A' and resid 479 through 508
    Processing helix  chain 'A' and resid 510 through 525
    Processing helix  chain 'A' and resid 525 through 554
    Processing helix  chain 'A' and resid 573 through 607
    Processing helix  chain 'B' and resid 29 through 51
    Processing helix  chain 'B' and resid 228 through 245
      removed outlier: 5.997A  pdb=" N   ARG B 234 " --> pdb=" O   MET B 230 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   TYR B 235 " --> pdb=" O   VAL B 231 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ARG B 238 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 309
    Processing helix  chain 'B' and resid 310 through 331
    Processing helix  chain 'B' and resid 333 through 336
    Processing helix  chain 'B' and resid 337 through 356
      removed outlier: 3.516A  pdb=" N   THR B 341 " --> pdb=" O   GLN B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 416
      removed outlier: 3.615A  pdb=" N   ILE B 393 " --> pdb=" O   VAL B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 430
    Processing helix  chain 'B' and resid 431 through 438
    Processing helix  chain 'B' and resid 439 through 466
      removed outlier: 3.544A  pdb=" N   VAL B 443 " --> pdb=" O   HIS B 439 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL B 453 " --> pdb=" O   ILE B 449 " (cutoff:3.500A)
      Proline residue:  B 456  - end of helix
    Processing helix  chain 'B' and resid 479 through 508
    Processing helix  chain 'B' and resid 510 through 525
    Processing helix  chain 'B' and resid 525 through 554
    Processing helix  chain 'B' and resid 573 through 607

    428 hydrogen bonds defined for protein.
    1260 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: 1.71

  Time building geometry restraints manager: 1.57 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 756
        1.30 -     1.43: 1504
        1.43 -     1.56: 3180
        1.56 -     1.68: 34
        1.68 -     1.81: 90
  Bond restraints: 5564
  Sorted by residual:
  bond pdb=" C   GLN B 337 "
       pdb=" O   GLN B 337 "
    ideal  model  delta    sigma   weight residual
    1.243  1.177  0.066 9.90e-03 1.02e+04 4.38e+01
  bond pdb=" C   GLN A 337 "
       pdb=" O   GLN A 337 "
    ideal  model  delta    sigma   weight residual
    1.243  1.178  0.065 9.90e-03 1.02e+04 4.35e+01
  bond pdb=" C   PHE B 339 "
       pdb=" O   PHE B 339 "
    ideal  model  delta    sigma   weight residual
    1.236  1.190  0.046 1.29e-02 6.01e+03 1.26e+01
  bond pdb=" C   PHE A 339 "
       pdb=" O   PHE A 339 "
    ideal  model  delta    sigma   weight residual
    1.236  1.190  0.046 1.29e-02 6.01e+03 1.25e+01
  bond pdb=" C17 CLR A 702 "
       pdb=" C20 CLR A 702 "
    ideal  model  delta    sigma   weight residual
    1.535  1.596 -0.061 2.00e-02 2.50e+03 9.18e+00
  ... (remaining 5559 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 7256
        2.16 -     4.32: 268
        4.32 -     6.48: 32
        6.48 -     8.64: 8
        8.64 -    10.80: 4
  Bond angle restraints: 7568
  Sorted by residual:
  angle pdb=" C   PHE B 339 "
        pdb=" N   TRP B 340 "
        pdb=" CA  TRP B 340 "
      ideal   model   delta    sigma   weight residual
     120.31  109.51   10.80 1.52e+00 4.33e-01 5.05e+01
  angle pdb=" C   PHE A 339 "
        pdb=" N   TRP A 340 "
        pdb=" CA  TRP A 340 "
      ideal   model   delta    sigma   weight residual
     120.31  109.53   10.78 1.52e+00 4.33e-01 5.03e+01
  angle pdb=" N   ILE A 428 "
        pdb=" CA  ILE A 428 "
        pdb=" C   ILE A 428 "
      ideal   model   delta    sigma   weight residual
     113.53  107.83    5.70 9.80e-01 1.04e+00 3.38e+01
  angle pdb=" N   ILE B 428 "
        pdb=" CA  ILE B 428 "
        pdb=" C   ILE B 428 "
      ideal   model   delta    sigma   weight residual
     113.53  107.85    5.68 9.80e-01 1.04e+00 3.36e+01
  angle pdb=" C   PHE B 336 "
        pdb=" N   GLN B 337 "
        pdb=" CA  GLN B 337 "
      ideal   model   delta    sigma   weight residual
     120.58  128.05   -7.47 1.32e+00 5.74e-01 3.20e+01
  ... (remaining 7563 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 3222
       17.14 -    34.28: 68
       34.28 -    51.42: 6
       51.42 -    68.56: 4
       68.56 -    85.70: 4
  Dihedral angle restraints: 3304
    sinusoidal: 1350
      harmonic: 1954
  Sorted by residual:
  dihedral pdb=" CA  TYR B 438 "
           pdb=" C   TYR B 438 "
           pdb=" N   HIS B 439 "
           pdb=" CA  HIS B 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.84  -20.16     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  TYR A 438 "
           pdb=" C   TYR A 438 "
           pdb=" N   HIS A 439 "
           pdb=" CA  HIS A 439 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.85  -20.15     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" CB  GLU B 591 "
           pdb=" CG  GLU B 591 "
           pdb=" CD  GLU B 591 "
           pdb=" OE1 GLU B 591 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.70   85.70     1      3.00e+01 1.11e-03 9.87e+00
  ... (remaining 3301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 642
       0.063 -    0.125: 240
       0.125 -    0.188: 32
       0.188 -    0.251: 8
       0.251 -    0.313: 8
  Chirality restraints: 930
  Sorted by residual:
  chirality pdb=" C13 CLR A 702 "
            pdb=" C12 CLR A 702 "
            pdb=" C14 CLR A 702 "
            pdb=" C17 CLR A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -3.25    0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" C13 CLR B 702 "
            pdb=" C12 CLR B 702 "
            pdb=" C14 CLR B 702 "
            pdb=" C17 CLR B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -3.25    0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" C14 CLR B 702 "
            pdb=" C13 CLR B 702 "
            pdb=" C15 CLR B 702 "
            pdb=" C8  CLR B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.63    0.31 2.00e-01 2.50e+01 2.38e+00
  ... (remaining 927 not shown)

  Planarity restraints: 860
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 343 "   -0.012 2.00e-02 2.50e+03   2.39e-02 5.71e+00
        pdb=" C   PHE A 343 "    0.041 2.00e-02 2.50e+03
        pdb=" O   PHE A 343 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ALA A 344 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 343 "    0.012 2.00e-02 2.50e+03   2.39e-02 5.70e+00
        pdb=" C   PHE B 343 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   PHE B 343 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ALA B 344 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 493 "    0.011 2.00e-02 2.50e+03   2.27e-02 5.17e+00
        pdb=" C   LEU B 493 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   LEU B 493 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASN B 494 "    0.013 2.00e-02 2.50e+03
  ... (remaining 857 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 2767
        2.99 -     3.47: 5843
        3.47 -     3.94: 8642
        3.94 -     4.42: 9683
        4.42 -     4.90: 15145
  Nonbonded interactions: 42080
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 326 "
            pdb=" OD2 ASP B 619 "
     model   vdw
     2.511 3.120
  nonbonded pdb=" NZ  LYS A 326 "
            pdb=" OD2 ASP A 619 "
     model   vdw
     2.512 3.120
  nonbonded pdb=" O   CYS B  26 "
            pdb=" OG1 THR B  27 "
     model   vdw
     2.531 3.040
  nonbonded pdb=" O   CYS A  26 "
            pdb=" OG1 THR A  27 "
     model   vdw
     2.531 3.040
  nonbonded pdb=" N   PHE B 336 "
            pdb=" N   GLN B 337 "
     model   vdw
     2.561 2.560
  ... (remaining 42075 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: 0.03
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:             0.860
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.990
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:3.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
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      :  0.008   0.066   5564  Z= 0.476
  Angle     :  0.969  10.801   7568  Z= 0.650
  Chirality :  0.066   0.313    930
  Planarity :  0.006   0.026    860
  Dihedral  :  9.324  85.703   2028
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 0.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.18 (0.31), residues: 642
  helix:  0.69 (0.21), residues: 518
  sheet:  None (None), residues: 0
  loop : -2.08 (0.51), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 386 
 HIS   0.001   0.000   HIS B 464 
 PHE   0.001   0.000   PHE B 348 
 TYR   0.001   0.000   TYR B 415 
 ARG   0.001   0.000   ARG B 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21072 (  428)
  hydrogen bonds       : angle       6.93898 ( 1260)
  covalent geometry    : bond        0.00825 ( 5564)
  covalent geometry    : angle       0.96944 ( 7568)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8669 (mt) cc_final: 0.8421 (mt)
REVERT: A  234 ARG cc_start: 0.7483 (ptt180) cc_final: 0.7161 (ptt-90)
REVERT: A  326 LYS cc_start: 0.8897 (mttt) cc_final: 0.8603 (ttmm)
REVERT: A  342 PHE cc_start: 0.7578 (t80) cc_final: 0.7357 (m-10)
REVERT: A  352 TRP cc_start: 0.8852 (t60) cc_final: 0.8616 (t60)
REVERT: A  354 MET cc_start: 0.8206 (mmm) cc_final: 0.7948 (tpp)
REVERT: A  438 TYR cc_start: 0.7244 (m-80) cc_final: 0.7021 (m-10)
REVERT: A  516 LYS cc_start: 0.6466 (mttt) cc_final: 0.6192 (mmtp)
REVERT: A  528 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7031 (mpt180)
REVERT: A  581 LEU cc_start: 0.8942 (mt) cc_final: 0.8654 (tt)
REVERT: B  340 TRP cc_start: 0.6592 (m-10) cc_final: 0.5815 (m100)
REVERT: B  437 ARG cc_start: 0.7457 (tpt90) cc_final: 0.6958 (mmt180)
REVERT: B  463 ILE cc_start: 0.8796 (mt) cc_final: 0.8568 (mm)
REVERT: B  508 SER cc_start: 0.8865 (m) cc_final: 0.8506 (t)
REVERT: B  516 LYS cc_start: 0.6949 (mttt) cc_final: 0.6379 (mptt)
REVERT: B  534 THR cc_start: 0.8810 (m) cc_final: 0.8596 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.1907
  time to fit residues: 69.5435
Evaluate side-chains
  178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:   10.0000
   chunk 17 optimal weight:    0.6980
   chunk 33 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 322 HIS
A 466 GLN
B 439 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.154974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.120133 restraints weight = 9006.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123419 restraints weight = 5596.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.125573 restraints weight = 4252.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5564  Z= 0.162
  Angle     :  0.680   7.472   7568  Z= 0.344
  Chirality :  0.039   0.184    930
  Planarity :  0.004   0.028    860
  Dihedral  :  4.735  31.905    836
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 14.93 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.68 (0.34), residues: 642
  helix:  2.65 (0.22), residues: 520
  sheet:  None (None), residues: 0
  loop : -2.41 (0.50), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 340 
 HIS   0.002   0.001   HIS B 330 
 PHE   0.020   0.001   PHE B  44 
 TYR   0.012   0.001   TYR B 415 
 ARG   0.006   0.001   ARG B 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05651 (  428)
  hydrogen bonds       : angle       4.24186 ( 1260)
  covalent geometry    : bond        0.00339 ( 5564)
  covalent geometry    : angle       0.68032 ( 7568)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 185
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 TYR cc_start: 0.7205 (m-80) cc_final: 0.6991 (m-80)
REVERT: A  342 PHE cc_start: 0.7881 (t80) cc_final: 0.7448 (m-10)
REVERT: A  397 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7722 (mp0)
REVERT: A  433 ASN cc_start: 0.7526 (p0) cc_final: 0.7158 (m-40)
REVERT: A  445 LYS cc_start: 0.8190 (tptm) cc_final: 0.7895 (tptm)
REVERT: A  528 ARG cc_start: 0.7912 (mtt90) cc_final: 0.7077 (mpt180)
REVERT: A  538 PHE cc_start: 0.8627 (t80) cc_final: 0.7727 (t80)
REVERT: A  542 LEU cc_start: 0.8732 (mp) cc_final: 0.8500 (mp)
REVERT: A  578 PHE cc_start: 0.8200 (t80) cc_final: 0.7780 (t80)
REVERT: A  581 LEU cc_start: 0.9001 (mt) cc_final: 0.8772 (tt)
REVERT: B   21 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7092 (pp)
REVERT: B   22 GLU cc_start: 0.7800 (mp0) cc_final: 0.7587 (mp0)
REVERT: B  234 ARG cc_start: 0.8782 (ptp90) cc_final: 0.8494 (ptp90)
REVERT: B  340 TRP cc_start: 0.6946 (m-10) cc_final: 0.6652 (m-10)
REVERT: B  508 SER cc_start: 0.8822 (m) cc_final: 0.8609 (t)
REVERT: B  516 LYS cc_start: 0.7089 (mttt) cc_final: 0.6312 (mmtt)
  outliers start: 38
  outliers final: 26
  residues processed: 216
  average time/residue: 0.1989
  time to fit residues: 55.4400
Evaluate side-chains
  181 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 153
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  396 SER
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  603 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 27 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.0782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.159459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.123423 restraints weight = 9078.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.126961 restraints weight = 5712.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.129253 restraints weight = 4368.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.5830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5564  Z= 0.149
  Angle     :  0.638   6.932   7568  Z= 0.321
  Chirality :  0.038   0.177    930
  Planarity :  0.004   0.031    860
  Dihedral  :  4.747  34.753    836
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 17.28 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.88 (0.34), residues: 642
  helix:  2.65 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -2.20 (0.59), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 352 
 HIS   0.004   0.001   HIS A 439 
 PHE   0.022   0.001   PHE B  48 
 TYR   0.027   0.002   TYR A 438 
 ARG   0.005   0.001   ARG B 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05109 (  428)
  hydrogen bonds       : angle       4.06187 ( 1260)
  covalent geometry    : bond        0.00333 ( 5564)
  covalent geometry    : angle       0.63752 ( 7568)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 173
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A  230 MET cc_start: 0.7991 (mmp) cc_final: 0.7639 (mmp)
REVERT: A  307 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7627 (tpt)
REVERT: A  342 PHE cc_start: 0.7823 (t80) cc_final: 0.7163 (m-10)
REVERT: A  349 TRP cc_start: 0.9064 (m-10) cc_final: 0.8861 (m-10)
REVERT: A  397 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7612 (mp0)
REVERT: A  466 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8691 (tm-30)
REVERT: A  501 TYR cc_start: 0.9220 (m-10) cc_final: 0.8962 (m-10)
REVERT: A  528 ARG cc_start: 0.7656 (mtt90) cc_final: 0.7207 (mpt180)
REVERT: A  538 PHE cc_start: 0.8664 (t80) cc_final: 0.7809 (t80)
REVERT: A  581 LEU cc_start: 0.9021 (mt) cc_final: 0.8666 (tt)
REVERT: B  244 LEU cc_start: 0.9091 (tt) cc_final: 0.8799 (mm)
REVERT: B  397 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8502 (mm-30)
REVERT: B  454 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8396 (ttpt)
REVERT: B  516 LYS cc_start: 0.7327 (mttt) cc_final: 0.6772 (mmtt)
  outliers start: 38
  outliers final: 20
  residues processed: 199
  average time/residue: 0.1477
  time to fit residues: 38.7487
Evaluate side-chains
  167 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 5 optimal weight:    0.0570
   chunk 56 optimal weight:    0.9980
   chunk 33 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0980
   chunk 50 optimal weight:    0.6980
   chunk 44 optimal weight:    0.3980
   overall best weight:    0.4098

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.161369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.128546 restraints weight = 9303.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.131537 restraints weight = 6288.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.133257 restraints weight = 4232.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.6499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5564  Z= 0.132
  Angle     :  0.632   8.842   7568  Z= 0.319
  Chirality :  0.038   0.201    930
  Planarity :  0.004   0.029    860
  Dihedral  :  4.639  29.025    836
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 22.65 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.78 (0.34), residues: 642
  helix:  2.58 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -2.21 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 352 
 HIS   0.001   0.000   HIS B 330 
 PHE   0.025   0.001   PHE B 343 
 TYR   0.023   0.002   TYR A 438 
 ARG   0.004   0.000   ARG B 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04331 (  428)
  hydrogen bonds       : angle       3.87735 ( 1260)
  covalent geometry    : bond        0.00275 ( 5564)
  covalent geometry    : angle       0.63244 ( 7568)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
REVERT: A  307 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7640 (tpt)
REVERT: A  342 PHE cc_start: 0.7797 (t80) cc_final: 0.7159 (m-10)
REVERT: A  349 TRP cc_start: 0.9036 (m-10) cc_final: 0.8675 (m-10)
REVERT: A  384 MET cc_start: 0.5125 (mpp) cc_final: 0.4709 (mpp)
REVERT: A  393 ILE cc_start: 0.8039 (mm) cc_final: 0.7783 (mt)
REVERT: A  397 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7484 (mp0)
REVERT: A  445 LYS cc_start: 0.8314 (tptm) cc_final: 0.7828 (tptm)
REVERT: A  449 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8907 (mp)
REVERT: A  501 TYR cc_start: 0.9212 (m-10) cc_final: 0.8998 (m-10)
REVERT: A  528 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7319 (mpt180)
REVERT: A  538 PHE cc_start: 0.8568 (t80) cc_final: 0.8172 (t80)
REVERT: A  581 LEU cc_start: 0.8949 (mt) cc_final: 0.8579 (tt)
REVERT: A  599 LEU cc_start: 0.8806 (tp) cc_final: 0.8491 (tp)
REVERT: B   42 MET cc_start: 0.8572 (tpt) cc_final: 0.8065 (tpp)
REVERT: B  242 TRP cc_start: 0.7607 (OUTLIER) cc_final: 0.6975 (t60)
REVERT: B  244 LEU cc_start: 0.8884 (tt) cc_final: 0.8628 (mm)
REVERT: B  419 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7044 (p0)
REVERT: B  438 TYR cc_start: 0.7773 (m-80) cc_final: 0.7272 (m-10)
REVERT: B  454 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8310 (ttmt)
REVERT: B  516 LYS cc_start: 0.7278 (mttt) cc_final: 0.6837 (mmtt)
  outliers start: 27
  outliers final: 15
  residues processed: 187
  average time/residue: 0.1705
  time to fit residues: 42.4916
Evaluate side-chains
  177 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  419 ASP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0980
   chunk 36 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    1.4188

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

Flipped N/Q/H residues before XYZ refinement:
A 466 GLN
B 608 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.150441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.116578 restraints weight = 9263.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.118314 restraints weight = 6736.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.120285 restraints weight = 5216.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.6878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5564  Z= 0.166
  Angle     :  0.660   7.827   7568  Z= 0.339
  Chirality :  0.040   0.245    930
  Planarity :  0.004   0.029    860
  Dihedral  :  5.242  41.099    836
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 21.81 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.79 (0.34), residues: 642
  helix:  2.65 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -2.06 (0.55), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 386 
 HIS   0.003   0.001   HIS B 330 
 PHE   0.024   0.002   PHE B 343 
 TYR   0.026   0.002   TYR A 438 
 ARG   0.003   0.001   ARG B 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05137 (  428)
  hydrogen bonds       : angle       4.04487 ( 1260)
  covalent geometry    : bond        0.00384 ( 5564)
  covalent geometry    : angle       0.66043 ( 7568)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 158
  time to evaluate  : 0.585 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7651 (OUTLIER) cc_final: 0.7168 (m-10)
REVERT: A  307 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7680 (tpt)
REVERT: A  342 PHE cc_start: 0.7845 (t80) cc_final: 0.7098 (m-10)
REVERT: A  349 TRP cc_start: 0.9127 (m-10) cc_final: 0.8896 (m-10)
REVERT: A  384 MET cc_start: 0.5364 (mpp) cc_final: 0.5109 (mpp)
REVERT: A  393 ILE cc_start: 0.8567 (mm) cc_final: 0.8131 (mt)
REVERT: A  397 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7436 (mp0)
REVERT: A  445 LYS cc_start: 0.8360 (tptm) cc_final: 0.7911 (tptm)
REVERT: A  449 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8826 (mp)
REVERT: A  458 MET cc_start: 0.7796 (tpt) cc_final: 0.7376 (tpt)
REVERT: A  538 PHE cc_start: 0.8678 (t80) cc_final: 0.8369 (t80)
REVERT: A  581 LEU cc_start: 0.9030 (mt) cc_final: 0.8633 (tt)
REVERT: B   42 MET cc_start: 0.8724 (tpt) cc_final: 0.8303 (tpp)
REVERT: B  242 TRP cc_start: 0.7603 (OUTLIER) cc_final: 0.6762 (t60)
REVERT: B  244 LEU cc_start: 0.8967 (tt) cc_final: 0.8764 (mm)
REVERT: B  516 LYS cc_start: 0.7267 (mttt) cc_final: 0.6712 (mmtt)
REVERT: B  604 ASP cc_start: 0.8933 (t70) cc_final: 0.8690 (t0)
  outliers start: 39
  outliers final: 25
  residues processed: 184
  average time/residue: 0.1493
  time to fit residues: 36.6960
Evaluate side-chains
  174 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.1986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.151171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.117997 restraints weight = 9267.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.120019 restraints weight = 6693.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.121777 restraints weight = 5077.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.7222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5564  Z= 0.148
  Angle     :  0.651   7.651   7568  Z= 0.329
  Chirality :  0.039   0.220    930
  Planarity :  0.004   0.027    860
  Dihedral  :  5.081  38.726    836
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 24.16 %
    Favored  : 69.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  2.82 (0.34), residues: 642
  helix:  2.66 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.98 (0.56), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 386 
 HIS   0.003   0.001   HIS B 330 
 PHE   0.023   0.001   PHE B 343 
 TYR   0.026   0.002   TYR A 438 
 ARG   0.003   0.001   ARG B 418 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04570 (  428)
  hydrogen bonds       : angle       3.94250 ( 1260)
  covalent geometry    : bond        0.00340 ( 5564)
  covalent geometry    : angle       0.65076 ( 7568)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 147
  time to evaluate  : 0.571 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7678 (OUTLIER) cc_final: 0.7130 (m-10)
REVERT: A  307 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7630 (tpt)
REVERT: A  342 PHE cc_start: 0.7825 (t80) cc_final: 0.7159 (m-10)
REVERT: A  349 TRP cc_start: 0.9140 (m-10) cc_final: 0.8932 (m-10)
REVERT: A  393 ILE cc_start: 0.8459 (mm) cc_final: 0.8019 (mt)
REVERT: A  397 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7324 (mp0)
REVERT: A  445 LYS cc_start: 0.8264 (tptm) cc_final: 0.7850 (tptm)
REVERT: A  449 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8800 (mp)
REVERT: A  458 MET cc_start: 0.7812 (tpt) cc_final: 0.7388 (tpt)
REVERT: A  581 LEU cc_start: 0.9006 (mt) cc_final: 0.8615 (tt)
REVERT: A  599 LEU cc_start: 0.8954 (tp) cc_final: 0.8443 (tt)
REVERT: B   42 MET cc_start: 0.8677 (tpt) cc_final: 0.8229 (tpp)
REVERT: B  230 MET cc_start: 0.8915 (mmm) cc_final: 0.8705 (mmt)
REVERT: B  242 TRP cc_start: 0.7523 (OUTLIER) cc_final: 0.6749 (t60)
REVERT: B  354 MET cc_start: 0.7193 (ttp) cc_final: 0.6799 (tmm)
REVERT: B  438 TYR cc_start: 0.7869 (m-80) cc_final: 0.7658 (m-10)
REVERT: B  516 LYS cc_start: 0.7407 (mttt) cc_final: 0.6894 (mmtt)
  outliers start: 39
  outliers final: 28
  residues processed: 173
  average time/residue: 0.1500
  time to fit residues: 34.5545
Evaluate side-chains
  175 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain A residue  620 LYS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  387 TYR
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 42 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.157152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.121979 restraints weight = 9178.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.125394 restraints weight = 5801.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.127437 restraints weight = 4415.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.7477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5564  Z= 0.134
  Angle     :  0.645   7.346   7568  Z= 0.324
  Chirality :  0.038   0.222    930
  Planarity :  0.004   0.027    860
  Dihedral  :  4.934  36.295    836
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 24.66 %
    Favored  : 68.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.01 (0.34), residues: 642
  helix:  2.79 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.90 (0.57), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 386 
 HIS   0.002   0.001   HIS B 330 
 PHE   0.024   0.001   PHE B 342 
 TYR   0.025   0.002   TYR A 438 
 ARG   0.004   0.001   ARG B 418 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04324 (  428)
  hydrogen bonds       : angle       3.85044 ( 1260)
  covalent geometry    : bond        0.00297 ( 5564)
  covalent geometry    : angle       0.64477 ( 7568)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 149
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.8426 (ttm) cc_final: 0.8211 (ttt)
REVERT: A  242 TRP cc_start: 0.7710 (OUTLIER) cc_final: 0.7176 (m-10)
REVERT: A  307 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7694 (tpt)
REVERT: A  349 TRP cc_start: 0.9126 (m-10) cc_final: 0.8771 (m-10)
REVERT: A  393 ILE cc_start: 0.8341 (mm) cc_final: 0.7894 (mt)
REVERT: A  397 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7321 (mp0)
REVERT: A  445 LYS cc_start: 0.8151 (tptm) cc_final: 0.7748 (tptm)
REVERT: A  449 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8751 (mp)
REVERT: A  458 MET cc_start: 0.7882 (tpt) cc_final: 0.7457 (tpt)
REVERT: A  460 LEU cc_start: 0.8554 (mp) cc_final: 0.8338 (tt)
REVERT: A  508 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8668 (t)
REVERT: A  516 LYS cc_start: 0.5961 (mmtp) cc_final: 0.5552 (mmtt)
REVERT: A  581 LEU cc_start: 0.8985 (mt) cc_final: 0.8612 (tt)
REVERT: A  599 LEU cc_start: 0.8842 (tp) cc_final: 0.8583 (tp)
REVERT: B   42 MET cc_start: 0.8662 (tpt) cc_final: 0.8226 (tpp)
REVERT: B  230 MET cc_start: 0.8887 (mmm) cc_final: 0.8628 (mmt)
REVERT: B  242 TRP cc_start: 0.7529 (OUTLIER) cc_final: 0.7003 (t60)
REVERT: B  354 MET cc_start: 0.7220 (ttp) cc_final: 0.6861 (tmm)
REVERT: B  438 TYR cc_start: 0.7908 (m-80) cc_final: 0.7506 (m-10)
REVERT: B  462 TYR cc_start: 0.8537 (t80) cc_final: 0.8057 (t80)
REVERT: B  516 LYS cc_start: 0.7369 (mttt) cc_final: 0.6898 (mmtt)
  outliers start: 38
  outliers final: 28
  residues processed: 177
  average time/residue: 0.1299
  time to fit residues: 31.1777
Evaluate side-chains
  173 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  620 LYS
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  387 TYR
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.157783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.125263 restraints weight = 9199.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.127818 restraints weight = 6264.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.129262 restraints weight = 4518.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.7631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5564  Z= 0.129
  Angle     :  0.637   8.516   7568  Z= 0.319
  Chirality :  0.038   0.201    930
  Planarity :  0.004   0.027    860
  Dihedral  :  4.792  32.690    836
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  6.88 %
    Allowed  : 24.83 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.02 (0.34), residues: 642
  helix:  2.89 (0.22), residues: 514
  sheet:  None (None), residues: 0
  loop : -2.07 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 386 
 HIS   0.002   0.000   HIS B 330 
 PHE   0.026   0.001   PHE B 343 
 TYR   0.021   0.002   TYR A 438 
 ARG   0.004   0.000   ARG B 418 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04126 (  428)
  hydrogen bonds       : angle       3.79575 ( 1260)
  covalent geometry    : bond        0.00280 ( 5564)
  covalent geometry    : angle       0.63687 ( 7568)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 148
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
REVERT: A  242 TRP cc_start: 0.7765 (OUTLIER) cc_final: 0.7238 (m-10)
REVERT: A  307 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7703 (tpt)
REVERT: A  342 PHE cc_start: 0.7799 (t80) cc_final: 0.7121 (m-10)
REVERT: A  349 TRP cc_start: 0.9120 (m-10) cc_final: 0.8763 (m-10)
REVERT: A  393 ILE cc_start: 0.8352 (mm) cc_final: 0.7922 (mt)
REVERT: A  397 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7309 (mp0)
REVERT: A  458 MET cc_start: 0.7765 (tpt) cc_final: 0.7438 (tpt)
REVERT: A  460 LEU cc_start: 0.8598 (mp) cc_final: 0.8308 (tt)
REVERT: A  508 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8626 (t)
REVERT: A  581 LEU cc_start: 0.8969 (mt) cc_final: 0.8558 (tt)
REVERT: A  599 LEU cc_start: 0.8871 (tp) cc_final: 0.8289 (tt)
REVERT: B  230 MET cc_start: 0.8825 (mmm) cc_final: 0.8592 (mmt)
REVERT: B  354 MET cc_start: 0.7303 (ttp) cc_final: 0.6832 (tmm)
REVERT: B  438 TYR cc_start: 0.7944 (m-80) cc_final: 0.7720 (m-10)
REVERT: B  462 TYR cc_start: 0.8598 (t80) cc_final: 0.8084 (t80)
REVERT: B  516 LYS cc_start: 0.7348 (mttt) cc_final: 0.6906 (mmtt)
REVERT: B  549 CYS cc_start: 0.8869 (m) cc_final: 0.8611 (m)
  outliers start: 41
  outliers final: 30
  residues processed: 177
  average time/residue: 0.1258
  time to fit residues: 30.8863
Evaluate side-chains
  180 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 146
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  386 TRP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  387 TYR
Chi-restraints excluded: chain B residue  419 ASP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   chunk 17 optimal weight:    0.6980
   chunk 60 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.152262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.120557 restraints weight = 9414.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.122784 restraints weight = 6377.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.123892 restraints weight = 4577.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.7813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5564  Z= 0.135
  Angle     :  0.663  10.457   7568  Z= 0.332
  Chirality :  0.039   0.240    930
  Planarity :  0.004   0.027    860
  Dihedral  :  4.794  31.392    836
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 25.34 %
    Favored  : 68.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.06 (0.34), residues: 642
  helix:  2.88 (0.22), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.84 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 386 
 HIS   0.003   0.001   HIS B 388 
 PHE   0.028   0.001   PHE B 342 
 TYR   0.025   0.002   TYR B 235 
 ARG   0.003   0.000   ARG B 418 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04257 (  428)
  hydrogen bonds       : angle       3.83715 ( 1260)
  covalent geometry    : bond        0.00300 ( 5564)
  covalent geometry    : angle       0.66276 ( 7568)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 150
  time to evaluate  : 0.584 
Fit side-chains
REVERT: A  242 TRP cc_start: 0.7736 (OUTLIER) cc_final: 0.7144 (m-10)
REVERT: A  307 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7705 (tpt)
REVERT: A  342 PHE cc_start: 0.7801 (t80) cc_final: 0.7119 (m-10)
REVERT: A  349 TRP cc_start: 0.9120 (m-10) cc_final: 0.8765 (m-10)
REVERT: A  393 ILE cc_start: 0.8393 (mm) cc_final: 0.7965 (mt)
REVERT: A  397 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7315 (mp0)
REVERT: A  458 MET cc_start: 0.7762 (tpt) cc_final: 0.7464 (tpt)
REVERT: A  460 LEU cc_start: 0.8583 (mp) cc_final: 0.8342 (tt)
REVERT: A  508 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8606 (t)
REVERT: A  538 PHE cc_start: 0.8650 (t80) cc_final: 0.7981 (t80)
REVERT: A  581 LEU cc_start: 0.8965 (mt) cc_final: 0.8553 (tt)
REVERT: A  599 LEU cc_start: 0.8886 (tp) cc_final: 0.8338 (tt)
REVERT: B  438 TYR cc_start: 0.7973 (m-80) cc_final: 0.7561 (m-10)
REVERT: B  462 TYR cc_start: 0.8571 (t80) cc_final: 0.8088 (t80)
REVERT: B  516 LYS cc_start: 0.7340 (mttt) cc_final: 0.6903 (mmtt)
REVERT: B  549 CYS cc_start: 0.8864 (m) cc_final: 0.8584 (m)
  outliers start: 39
  outliers final: 28
  residues processed: 179
  average time/residue: 0.1313
  time to fit residues: 32.5891
Evaluate side-chains
  179 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 147
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.151833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.120204 restraints weight = 9412.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.122588 restraints weight = 6332.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.123688 restraints weight = 4524.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.7865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5564  Z= 0.137
  Angle     :  0.681  10.404   7568  Z= 0.336
  Chirality :  0.039   0.236    930
  Planarity :  0.004   0.031    860
  Dihedral  :  4.793  30.031    836
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 25.84 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.00 (0.34), residues: 642
  helix:  2.84 (0.22), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.90 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 385 
 HIS   0.002   0.001   HIS B 330 
 PHE   0.017   0.001   PHE A 578 
 TYR   0.020   0.002   TYR A 438 
 ARG   0.004   0.000   ARG B 418 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04232 (  428)
  hydrogen bonds       : angle       3.86220 ( 1260)
  covalent geometry    : bond        0.00307 ( 5564)
  covalent geometry    : angle       0.68107 ( 7568)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 148
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
REVERT: A  242 TRP cc_start: 0.7735 (OUTLIER) cc_final: 0.7213 (m-10)
REVERT: A  307 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7706 (tpt)
REVERT: A  342 PHE cc_start: 0.7777 (t80) cc_final: 0.7083 (m-10)
REVERT: A  349 TRP cc_start: 0.9130 (m-10) cc_final: 0.8771 (m-10)
REVERT: A  393 ILE cc_start: 0.8428 (mm) cc_final: 0.7990 (mt)
REVERT: A  397 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7345 (mp0)
REVERT: A  458 MET cc_start: 0.7778 (tpt) cc_final: 0.7494 (tpt)
REVERT: A  460 LEU cc_start: 0.8564 (mp) cc_final: 0.8322 (tt)
REVERT: A  508 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8609 (t)
REVERT: A  538 PHE cc_start: 0.8634 (t80) cc_final: 0.8179 (t80)
REVERT: A  581 LEU cc_start: 0.8978 (mt) cc_final: 0.8602 (tt)
REVERT: A  599 LEU cc_start: 0.8860 (tp) cc_final: 0.8297 (tt)
REVERT: B  354 MET cc_start: 0.7432 (ttp) cc_final: 0.6864 (tmm)
REVERT: B  438 TYR cc_start: 0.7907 (m-80) cc_final: 0.7516 (m-10)
REVERT: B  462 TYR cc_start: 0.8583 (t80) cc_final: 0.8097 (t80)
REVERT: B  516 LYS cc_start: 0.7345 (mttt) cc_final: 0.6910 (mmtt)
REVERT: B  539 MET cc_start: 0.8817 (mtp) cc_final: 0.8561 (ttm)
REVERT: B  549 CYS cc_start: 0.8831 (m) cc_final: 0.8485 (m)
  outliers start: 35
  outliers final: 29
  residues processed: 175
  average time/residue: 0.1415
  time to fit residues: 34.4306
Evaluate side-chains
  175 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  419 ASP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  545 VAL
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  605 THR
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 42 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 533 ASN ** 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 = 0.3907 r_free = 0.3907 target = 0.157308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.122996 restraints weight = 9225.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.126341 restraints weight = 5814.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.128325 restraints weight = 4420.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.8012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   5564  Z= 0.133
  Angle     :  0.669  10.366   7568  Z= 0.331
  Chirality :  0.039   0.236    930
  Planarity :  0.004   0.025    860
  Dihedral  :  4.755  30.978    836
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 26.85 %
    Favored  : 67.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.04 (0.34), residues: 642
  helix:  2.93 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.00 (0.56), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 386 
 HIS   0.002   0.000   HIS B 330 
 PHE   0.030   0.001   PHE B 342 
 TYR   0.020   0.002   TYR B 351 
 ARG   0.004   0.000   ARG B 418 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04101 (  428)
  hydrogen bonds       : angle       3.84315 ( 1260)
  covalent geometry    : bond        0.00295 ( 5564)
  covalent geometry    : angle       0.66887 ( 7568)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1987.27 seconds
wall clock time: 35 minutes 56.99 seconds (2156.99 seconds total)