Starting phenix.real_space_refine
on Fri May  9 21:59:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ji0_36303/05_2025/8ji0_36303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ji0_36303/05_2025/8ji0_36303.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ji0_36303/05_2025/8ji0_36303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ji0_36303/05_2025/8ji0_36303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ji0_36303/05_2025/8ji0_36303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ji0_36303/05_2025/8ji0_36303.cif"
  }
  resolution = 3.0
  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=  -0.001 sd=   0.100
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      24      5.16       5
     C    2512      2.51       5
     N     665      2.21       5
     O     733      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3934
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 2669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2669
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 324}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1265
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 6, 'TRANS': 150}
  Time building chain proxies: 2.87, per 1000 atoms: 0.73
  Number of scatterers: 3934
  At special positions: 0
  Unit cell: (81.525, 83.699, 81.525, 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      24     16.00
     O     733      8.00
     N     665      7.00
     C    2512      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 231 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 185 " - pdb=" SG  CYS B 241 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 244 " - pdb=" SG  CYS B 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 281 " - pdb=" SG  CYS B 297 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 410 " - pdb=" SG  CYS B 426 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 497.7 milliseconds
  

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  900

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 11 sheets defined
      10.2% alpha, 25.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'B' and resid 177 through 188
      removed outlier: 3.588A  pdb=" N   GLY B 181 " --> pdb=" O   ASN B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 225
      removed outlier: 3.616A  pdb=" N   LYS B 224 " --> pdb=" O   ASP B 220 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU B 225 " --> pdb=" O   ILE B 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 220 through 225'
    Processing helix  chain 'B' and resid 294 through 299
      removed outlier: 4.013A  pdb=" N   VAL B 298 " --> pdb=" O   ALA B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 320
    Processing helix  chain 'B' and resid 406 through 411
    Processing helix  chain 'B' and resid 477 through 492
      removed outlier: 4.795A  pdb=" N   ASP B 482 " --> pdb=" O   MET B 478 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   TRP B 483 " --> pdb=" O   VAL B 479 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 149 through 152
    Processing sheet with id=AA2, first strand: chain 'B' and resid 196 through 201
    Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 282
      removed outlier: 3.673A  pdb=" N   CYS B 281 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   TRP B 290 " --> pdb=" O   ILE B 286 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 379 through 383
      removed outlier: 3.527A  pdb=" N   GLY B 383 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASN B 398 " --> pdb=" O   GLY B 383 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   CYS B 426 " --> pdb=" O   ILE B 405 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B 473 " --> pdb=" O   SER B 460 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LEU B 445 " --> pdb=" O   ILE B 456 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   SER B 382 " --> pdb=" O   PRO B 444 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2462 through 2466
      removed outlier: 3.641A  pdb=" N   LYS A2462 " --> pdb=" O   PHE A2473 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2484 through 2486
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2502 through 2507
      removed outlier: 3.505A  pdb=" N   LYS A2505 " --> pdb=" O   PHE A2512 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A2512 " --> pdb=" O   LYS A2505 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2522 through 2523
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2553 through 2557
      removed outlier: 3.854A  pdb=" N   LYS A2553 " --> pdb=" O   PHE A2564 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   PHE A2564 " --> pdb=" O   LYS A2553 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2573 through 2577
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2595 through 2597
      removed outlier: 3.689A  pdb=" N   PHE A2606 " --> pdb=" O   GLY A2595 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   PHE A2605 " --> pdb=" O   GLN A2613 " (cutoff:3.500A)

    104 hydrogen bonds defined for protein.
    246 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.96

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.04 -     1.20: 13
        1.20 -     1.35: 1258
        1.35 -     1.51: 1295
        1.51 -     1.66: 1447
        1.66 -     1.81: 34
  Bond restraints: 4047
  Sorted by residual:
  bond pdb=" C   ASN B 304 "
       pdb=" O   ASN B 304 "
    ideal  model  delta    sigma   weight residual
    1.235  1.045  0.190 1.45e-02 4.76e+03 1.72e+02
  bond pdb=" C   PRO B 301 "
       pdb=" O   PRO B 301 "
    ideal  model  delta    sigma   weight residual
    1.237  1.115  0.122 1.20e-02 6.94e+03 1.04e+02
  bond pdb=" C   TRP B 306 "
       pdb=" O   TRP B 306 "
    ideal  model  delta    sigma   weight residual
    1.236  1.117  0.119 1.23e-02 6.61e+03 9.39e+01
  bond pdb=" C   PRO B 305 "
       pdb=" O   PRO B 305 "
    ideal  model  delta    sigma   weight residual
    1.235  1.111  0.124 1.30e-02 5.92e+03 9.04e+01
  bond pdb=" C   ASN B 303 "
       pdb=" O   ASN B 303 "
    ideal  model  delta    sigma   weight residual
    1.237  1.122  0.115 1.39e-02 5.18e+03 6.88e+01
  ... (remaining 4042 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.14: 5422
        4.14 -     8.29: 54
        8.29 -    12.43: 12
       12.43 -    16.57: 7
       16.57 -    20.72: 2
  Bond angle restraints: 5497
  Sorted by residual:
  angle pdb=" N   TYR B 414 "
        pdb=" CA  TYR B 414 "
        pdb=" C   TYR B 414 "
      ideal   model   delta    sigma   weight residual
     114.16   93.44   20.72 1.48e+00 4.57e-01 1.96e+02
  angle pdb=" N   TRP B 306 "
        pdb=" CA  TRP B 306 "
        pdb=" CB  TRP B 306 "
      ideal   model   delta    sigma   weight residual
     110.98   97.28   13.70 1.32e+00 5.74e-01 1.08e+02
  angle pdb=" C   PRO B 305 "
        pdb=" CA  PRO B 305 "
        pdb=" CB  PRO B 305 "
      ideal   model   delta    sigma   weight residual
     111.56   95.17   16.39 1.65e+00 3.67e-01 9.87e+01
  angle pdb=" C   TRP B 306 "
        pdb=" CA  TRP B 306 "
        pdb=" CB  TRP B 306 "
      ideal   model   delta    sigma   weight residual
     109.27  123.51  -14.24 1.64e+00 3.72e-01 7.54e+01
  angle pdb=" CB  LYS B 342 "
        pdb=" CG  LYS B 342 "
        pdb=" CD  LYS B 342 "
      ideal   model   delta    sigma   weight residual
     111.30   91.65   19.65 2.30e+00 1.89e-01 7.30e+01
  ... (remaining 5492 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.41: 1927
       14.41 -    28.82: 275
       28.82 -    43.23: 91
       43.23 -    57.64: 37
       57.64 -    72.05: 9
  Dihedral angle restraints: 2339
    sinusoidal: 917
      harmonic: 1422
  Sorted by residual:
  dihedral pdb=" C   ILE A2608 "
           pdb=" N   ILE A2608 "
           pdb=" CA  ILE A2608 "
           pdb=" CB  ILE A2608 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -148.04   26.04     0      2.50e+00 1.60e-01 1.08e+02
  dihedral pdb=" C   LYS B 342 "
           pdb=" N   LYS B 342 "
           pdb=" CA  LYS B 342 "
           pdb=" CB  LYS B 342 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -145.93   23.33     0      2.50e+00 1.60e-01 8.71e+01
  dihedral pdb=" N   ILE A2608 "
           pdb=" C   ILE A2608 "
           pdb=" CA  ILE A2608 "
           pdb=" CB  ILE A2608 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  143.42  -20.02     0      2.50e+00 1.60e-01 6.42e+01
  ... (remaining 2336 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.202: 553
       0.202 -    0.404: 4
       0.404 -    0.606: 3
       0.606 -    0.808: 1
       0.808 -    1.010: 2
  Chirality restraints: 563
  Sorted by residual:
  chirality pdb=" CA  LYS B 342 "
            pdb=" N   LYS B 342 "
            pdb=" C   LYS B 342 "
            pdb=" CB  LYS B 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.50    1.01 2.00e-01 2.50e+01 2.55e+01
  chirality pdb=" CA  ILE A2608 "
            pdb=" N   ILE A2608 "
            pdb=" C   ILE A2608 "
            pdb=" CB  ILE A2608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.61    0.82 2.00e-01 2.50e+01 1.70e+01
  chirality pdb=" CA  ARG B 413 "
            pdb=" N   ARG B 413 "
            pdb=" C   ARG B 413 "
            pdb=" CB  ARG B 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.78    0.73 2.00e-01 2.50e+01 1.35e+01
  ... (remaining 560 not shown)

  Planarity restraints: 717
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 306 "    0.032 2.00e-02 2.50e+03   6.87e-02 4.72e+01
        pdb=" C   TRP B 306 "   -0.119 2.00e-02 2.50e+03
        pdb=" O   TRP B 306 "    0.047 2.00e-02 2.50e+03
        pdb=" N   HIS B 307 "    0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 300 "    0.028 2.00e-02 2.50e+03   5.61e-02 3.15e+01
        pdb=" C   LYS B 300 "   -0.097 2.00e-02 2.50e+03
        pdb=" O   LYS B 300 "    0.036 2.00e-02 2.50e+03
        pdb=" N   PRO B 301 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 414 "    0.023 2.00e-02 2.50e+03   4.99e-02 2.49e+01
        pdb=" C   TYR B 414 "   -0.086 2.00e-02 2.50e+03
        pdb=" O   TYR B 414 "    0.034 2.00e-02 2.50e+03
        pdb=" N   VAL B 415 "    0.029 2.00e-02 2.50e+03
  ... (remaining 714 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.50: 38
        2.50 -     3.10: 2929
        3.10 -     3.70: 5689
        3.70 -     4.30: 8474
        4.30 -     4.90: 14441
  Nonbonded interactions: 31571
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 416 "
            pdb=" O   PRO B 471 "
     model   vdw
     1.905 3.040
  nonbonded pdb=" OG1 THR A2506 "
            pdb=" OD1 ASN A2511 "
     model   vdw
     1.965 3.040
  nonbonded pdb=" OH  TYR A2550 "
            pdb=" O   PHE A2554 "
     model   vdw
     2.001 3.040
  nonbonded pdb=" O   LYS B 300 "
            pdb=" NZ  LYS B 300 "
     model   vdw
     2.035 3.120
  nonbonded pdb=" O   MET B 371 "
            pdb=" NZ  LYS B 449 "
     model   vdw
     2.067 3.120
  ... (remaining 31566 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.420
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
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      :  0.009   0.190   4052  Z= 0.587
  Angle     :  1.196  20.716   5507  Z= 0.724
  Chirality :  0.089   1.010    563
  Planarity :  0.007   0.069    717
  Dihedral  : 16.497  72.050   1424
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  8.94 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  6.46 %
    Allowed  : 22.73 %
    Favored  : 70.81 %
  Cbeta Deviations :  1.78 %
  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: -1.71 (0.39), residues: 492
  helix: -1.24 (0.87), residues: 36
  sheet: -2.20 (0.47), residues: 114
  loop : -0.70 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B 306 
 HIS   0.004   0.001   HIS B 296 
 PHE   0.008   0.001   PHE B 156 
 TYR   0.038   0.002   TYR B 414 
 ARG   0.006   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24372 (  104)
  hydrogen bonds       : angle      10.25244 (  246)
  SS BOND              : bond        0.00225 (    5)
  SS BOND              : angle       0.89427 (   10)
  covalent geometry    : bond        0.00929 ( 4047)
  covalent geometry    : angle       1.19679 ( 5497)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
REVERT: B  329 GLU cc_start: 0.6891 (pp20) cc_final: 0.6635 (pp20)
REVERT: A 2515 ARG cc_start: 0.6933 (tpp80) cc_final: 0.6678 (tpt170)
REVERT: A 2612 LYS cc_start: 0.7175 (ttpp) cc_final: 0.6955 (ttpt)
  outliers start: 27
  outliers final: 15
  residues processed: 102
  average time/residue: 0.8699
  time to fit residues: 92.5501
Evaluate side-chains
  78 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 ASN
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  204 SER
Chi-restraints excluded: chain B residue  227 HIS
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  306 TRP
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  413 ARG
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  441 SER
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain A residue 2508 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 37 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0570
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.7302

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

Flipped N/Q/H residues before XYZ refinement:
B 450 ASN
B 451 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.246870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.214548 restraints weight = 4128.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.4583 rms_B_bonded: 2.20
r_work: 0.4437 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.4437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4052  Z= 0.161
  Angle     :  0.678   9.380   5507  Z= 0.359
  Chirality :  0.049   0.198    563
  Planarity :  0.005   0.074    717
  Dihedral  :  9.041  77.759    564
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  7.72 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 25.12 %
    Favored  : 70.33 %
  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: -1.12 (0.39), residues: 492
  helix: -0.28 (0.90), residues: 36
  sheet: -2.02 (0.50), residues: 95
  loop : -0.38 (0.35), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 306 
 HIS   0.006   0.001   HIS B 296 
 PHE   0.013   0.001   PHE A2466 
 TYR   0.029   0.002   TYR A2563 
 ARG   0.003   0.000   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04254 (  104)
  hydrogen bonds       : angle       6.84387 (  246)
  SS BOND              : bond        0.00332 (    5)
  SS BOND              : angle       1.08940 (   10)
  covalent geometry    : bond        0.00369 ( 4047)
  covalent geometry    : angle       0.67737 ( 5497)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
REVERT: B  210 MET cc_start: 0.7228 (mmm) cc_final: 0.6995 (mmt)
REVERT: B  329 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6812 (pp20)
REVERT: B  488 MET cc_start: 0.7297 (mtp) cc_final: 0.6626 (mpp)
REVERT: A 2515 ARG cc_start: 0.6852 (tpp80) cc_final: 0.6525 (tpt170)
REVERT: A 2612 LYS cc_start: 0.7394 (ttpp) cc_final: 0.7019 (ttpt)
REVERT: A 2613 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6840 (mt0)
  outliers start: 19
  outliers final: 8
  residues processed: 78
  average time/residue: 0.9824
  time to fit residues: 80.1517
Evaluate side-chains
  73 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  227 HIS
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain A residue 2588 THR
Chi-restraints excluded: chain A residue 2613 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 336 ASN
B 450 ASN
A2540 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.247469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.215589 restraints weight = 4128.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.4601 rms_B_bonded: 2.16
r_work: 0.4454 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.4293 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.4293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4052  Z= 0.133
  Angle     :  0.601   6.233   5507  Z= 0.321
  Chirality :  0.048   0.200    563
  Planarity :  0.005   0.050    717
  Dihedral  :  6.768  52.567    547
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 23.44 %
    Favored  : 72.01 %
  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: -0.82 (0.40), residues: 492
  helix:  0.12 (0.95), residues: 36
  sheet: -1.53 (0.53), residues: 94
  loop : -0.29 (0.35), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 461 
 HIS   0.005   0.001   HIS B 296 
 PHE   0.008   0.001   PHE A2466 
 TYR   0.020   0.002   TYR A2563 
 ARG   0.003   0.000   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03390 (  104)
  hydrogen bonds       : angle       6.35482 (  246)
  SS BOND              : bond        0.00199 (    5)
  SS BOND              : angle       0.83583 (   10)
  covalent geometry    : bond        0.00301 ( 4047)
  covalent geometry    : angle       0.60037 ( 5497)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: B  488 MET cc_start: 0.7308 (mtp) cc_final: 0.6578 (mpp)
REVERT: A 2515 ARG cc_start: 0.7018 (tpp80) cc_final: 0.6699 (tpt170)
REVERT: A 2612 LYS cc_start: 0.7558 (ttpp) cc_final: 0.7002 (ttpt)
  outliers start: 19
  outliers final: 7
  residues processed: 82
  average time/residue: 0.9790
  time to fit residues: 83.6293
Evaluate side-chains
  68 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain A residue 2588 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B 450 ASN
A2516 ASN
A2546 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4805 r_free = 0.4805 target = 0.240210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.210012 restraints weight = 4206.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.4563 rms_B_bonded: 2.05
r_work: 0.4408 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.4249 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   4052  Z= 0.216
  Angle     :  0.686   7.066   5507  Z= 0.366
  Chirality :  0.051   0.185    563
  Planarity :  0.005   0.046    717
  Dihedral  :  7.072  55.841    545
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 23.92 %
    Favored  : 70.81 %
  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: -1.08 (0.39), residues: 492
  helix: -0.33 (0.89), residues: 36
  sheet: -1.53 (0.45), residues: 131
  loop : -0.32 (0.37), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 380 
 HIS   0.005   0.001   HIS B 296 
 PHE   0.010   0.002   PHE A2521 
 TYR   0.023   0.002   TYR A2563 
 ARG   0.004   0.001   ARG B 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04111 (  104)
  hydrogen bonds       : angle       6.70183 (  246)
  SS BOND              : bond        0.00302 (    5)
  SS BOND              : angle       1.28871 (   10)
  covalent geometry    : bond        0.00509 ( 4047)
  covalent geometry    : angle       0.68475 ( 5497)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: B  165 ARG cc_start: 0.7031 (mtt180) cc_final: 0.6728 (mtm180)
REVERT: B  329 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7089 (pp20)
REVERT: B  413 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7174 (ptp90)
REVERT: B  488 MET cc_start: 0.7315 (mtp) cc_final: 0.6799 (mpp)
REVERT: A 2515 ARG cc_start: 0.7027 (tpp80) cc_final: 0.6728 (tpt170)
REVERT: A 2612 LYS cc_start: 0.7582 (ttpp) cc_final: 0.7027 (ttpp)
  outliers start: 22
  outliers final: 12
  residues processed: 84
  average time/residue: 0.9913
  time to fit residues: 86.9911
Evaluate side-chains
  74 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  204 SER
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  413 ARG
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  441 SER
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain A residue 2588 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 296 HIS
B 336 ASN
B 450 ASN
A2516 ASN
A2540 ASN
A2546 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4830 r_free = 0.4830 target = 0.243389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.213053 restraints weight = 4295.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.4557 rms_B_bonded: 2.07
r_work: 0.4412 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4257 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4052  Z= 0.164
  Angle     :  0.640   6.079   5507  Z= 0.341
  Chirality :  0.049   0.175    563
  Planarity :  0.005   0.044    717
  Dihedral  :  6.808  57.093    545
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 24.16 %
    Favored  : 70.57 %
  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: -1.01 (0.40), residues: 492
  helix: -0.17 (0.92), residues: 36
  sheet: -1.48 (0.45), residues: 131
  loop : -0.29 (0.37), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 380 
 HIS   0.005   0.001   HIS B 296 
 PHE   0.007   0.001   PHE A2533 
 TYR   0.029   0.002   TYR A2563 
 ARG   0.003   0.001   ARG B 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03589 (  104)
  hydrogen bonds       : angle       6.51952 (  246)
  SS BOND              : bond        0.00206 (    5)
  SS BOND              : angle       0.98554 (   10)
  covalent geometry    : bond        0.00378 ( 4047)
  covalent geometry    : angle       0.63887 ( 5497)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: B  329 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7076 (pp20)
REVERT: B  401 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8342 (ttpp)
REVERT: B  413 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6926 (ptp90)
REVERT: B  488 MET cc_start: 0.7179 (mtp) cc_final: 0.6770 (mpp)
REVERT: A 2515 ARG cc_start: 0.6988 (tpp80) cc_final: 0.6662 (tpt170)
REVERT: A 2612 LYS cc_start: 0.7552 (ttpp) cc_final: 0.6999 (ttpt)
  outliers start: 22
  outliers final: 12
  residues processed: 77
  average time/residue: 0.8514
  time to fit residues: 68.5252
Evaluate side-chains
  77 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  401 LYS
Chi-restraints excluded: chain B residue  413 ARG
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  441 SER
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain A residue 2588 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 42 optimal weight:    0.2980
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 227 HIS
B 450 ASN
A2540 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4823 r_free = 0.4823 target = 0.242785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.212383 restraints weight = 4139.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.4555 rms_B_bonded: 2.04
r_work: 0.4418 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.4260 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4052  Z= 0.174
  Angle     :  0.652   5.834   5507  Z= 0.345
  Chirality :  0.050   0.175    563
  Planarity :  0.005   0.043    717
  Dihedral  :  6.868  57.398    545
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  6.22 %
    Allowed  : 23.21 %
    Favored  : 70.57 %
  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: -1.01 (0.40), residues: 492
  helix: -0.26 (0.91), residues: 36
  sheet: -1.52 (0.45), residues: 131
  loop : -0.25 (0.37), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 380 
 HIS   0.008   0.001   HIS B 296 
 PHE   0.007   0.001   PHE B 156 
 TYR   0.027   0.002   TYR A2563 
 ARG   0.003   0.000   ARG B 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03593 (  104)
  hydrogen bonds       : angle       6.53657 (  246)
  SS BOND              : bond        0.00231 (    5)
  SS BOND              : angle       1.05159 (   10)
  covalent geometry    : bond        0.00406 ( 4047)
  covalent geometry    : angle       0.65065 ( 5497)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 67
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: B  164 GLN cc_start: 0.6300 (OUTLIER) cc_final: 0.6085 (pp30)
REVERT: B  186 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7910 (mtp85)
REVERT: B  329 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7148 (pp20)
REVERT: B  401 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8346 (ttpp)
REVERT: B  413 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7215 (ptp90)
REVERT: B  488 MET cc_start: 0.7191 (mtp) cc_final: 0.6777 (mpp)
REVERT: A 2515 ARG cc_start: 0.7067 (tpp80) cc_final: 0.6759 (tpt170)
REVERT: A 2531 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7084 (mt-10)
REVERT: A 2612 LYS cc_start: 0.7541 (ttpp) cc_final: 0.6965 (ttpt)
  outliers start: 26
  outliers final: 11
  residues processed: 84
  average time/residue: 0.9379
  time to fit residues: 82.0953
Evaluate side-chains
  80 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 GLN
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  401 LYS
Chi-restraints excluded: chain B residue  413 ARG
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  441 SER
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain A residue 2588 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0050
   chunk 24 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
B 450 ASN
A2540 ASN
A2546 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4837 r_free = 0.4837 target = 0.243575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.212502 restraints weight = 4116.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.4571 rms_B_bonded: 2.06
r_work: 0.4433 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.4275 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.4275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4052  Z= 0.151
  Angle     :  0.642   7.512   5507  Z= 0.341
  Chirality :  0.049   0.178    563
  Planarity :  0.005   0.044    717
  Dihedral  :  6.594  54.988    545
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 23.92 %
    Favored  : 70.33 %
  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: -0.91 (0.40), residues: 492
  helix:  0.17 (0.96), residues: 36
  sheet: -1.49 (0.47), residues: 118
  loop : -0.29 (0.37), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 380 
 HIS   0.006   0.001   HIS B 296 
 PHE   0.006   0.001   PHE B 156 
 TYR   0.023   0.002   TYR A2563 
 ARG   0.002   0.000   ARG B 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03366 (  104)
  hydrogen bonds       : angle       6.42149 (  246)
  SS BOND              : bond        0.00158 (    5)
  SS BOND              : angle       0.85951 (   10)
  covalent geometry    : bond        0.00345 ( 4047)
  covalent geometry    : angle       0.64134 ( 5497)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: B  186 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7814 (mtp85)
REVERT: B  329 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7104 (pp20)
REVERT: B  371 MET cc_start: 0.7657 (mmm) cc_final: 0.7140 (mmt)
REVERT: B  401 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8358 (ttpp)
REVERT: B  413 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6903 (ptp90)
REVERT: B  470 ARG cc_start: 0.5994 (mpt180) cc_final: 0.5789 (mpp-170)
REVERT: B  488 MET cc_start: 0.7210 (mtp) cc_final: 0.6792 (mpp)
REVERT: A 2515 ARG cc_start: 0.7080 (tpp80) cc_final: 0.6787 (tpt170)
REVERT: A 2531 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7103 (mt-10)
REVERT: A 2612 LYS cc_start: 0.7514 (ttpp) cc_final: 0.6957 (ttpt)
  outliers start: 24
  outliers final: 12
  residues processed: 83
  average time/residue: 0.8838
  time to fit residues: 76.4941
Evaluate side-chains
  81 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  401 LYS
Chi-restraints excluded: chain B residue  413 ARG
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  441 SER
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain A residue 2588 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 450 ASN
A2516 ASN
A2540 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4837 r_free = 0.4837 target = 0.243873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.213817 restraints weight = 4105.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.4549 rms_B_bonded: 2.02
r_work: 0.4424 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.4270 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4052  Z= 0.176
  Angle     :  0.660   6.559   5507  Z= 0.352
  Chirality :  0.050   0.174    563
  Planarity :  0.005   0.043    717
  Dihedral  :  6.785  55.486    545
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 25.12 %
    Favored  : 69.86 %
  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: -0.97 (0.40), residues: 492
  helix:  0.09 (0.96), residues: 36
  sheet: -1.49 (0.45), residues: 131
  loop : -0.27 (0.37), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 380 
 HIS   0.008   0.001   HIS B 296 
 PHE   0.008   0.001   PHE B 156 
 TYR   0.024   0.002   TYR A2563 
 ARG   0.003   0.000   ARG B 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03543 (  104)
  hydrogen bonds       : angle       6.53283 (  246)
  SS BOND              : bond        0.00212 (    5)
  SS BOND              : angle       1.00879 (   10)
  covalent geometry    : bond        0.00409 ( 4047)
  covalent geometry    : angle       0.65938 ( 5497)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: B  186 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7885 (mtp85)
REVERT: B  329 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7124 (pp20)
REVERT: B  401 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8326 (ttpp)
REVERT: B  413 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7175 (ptp90)
REVERT: B  488 MET cc_start: 0.7227 (mtp) cc_final: 0.6786 (mpp)
REVERT: A 2515 ARG cc_start: 0.7103 (tpp80) cc_final: 0.6780 (tpt170)
REVERT: A 2531 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7120 (mt-10)
REVERT: A 2612 LYS cc_start: 0.7493 (ttpp) cc_final: 0.6905 (ttpt)
  outliers start: 21
  outliers final: 13
  residues processed: 81
  average time/residue: 0.9749
  time to fit residues: 82.2676
Evaluate side-chains
  83 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  401 LYS
Chi-restraints excluded: chain B residue  413 ARG
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  441 SER
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain A residue 2588 THR
Chi-restraints excluded: chain A residue 2600 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0030
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
B 450 ASN
A2516 ASN
A2540 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4840 r_free = 0.4840 target = 0.243943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.213058 restraints weight = 4142.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.4582 rms_B_bonded: 2.05
r_work: 0.4448 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.4289 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4052  Z= 0.145
  Angle     :  0.635   7.350   5507  Z= 0.339
  Chirality :  0.049   0.173    563
  Planarity :  0.005   0.046    717
  Dihedral  :  6.524  55.670    545
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 26.32 %
    Favored  : 69.14 %
  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: -0.88 (0.40), residues: 492
  helix:  0.16 (0.95), residues: 36
  sheet: -1.46 (0.45), residues: 131
  loop : -0.20 (0.38), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 380 
 HIS   0.006   0.001   HIS B 296 
 PHE   0.006   0.001   PHE B 156 
 TYR   0.023   0.002   TYR B 485 
 ARG   0.003   0.000   ARG B 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03239 (  104)
  hydrogen bonds       : angle       6.39107 (  246)
  SS BOND              : bond        0.00138 (    5)
  SS BOND              : angle       0.81328 (   10)
  covalent geometry    : bond        0.00333 ( 4047)
  covalent geometry    : angle       0.63476 ( 5497)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: B  186 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7830 (mtp85)
REVERT: B  329 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7106 (pp20)
REVERT: B  401 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8300 (ttpp)
REVERT: B  488 MET cc_start: 0.7305 (mtp) cc_final: 0.6881 (mpp)
REVERT: A 2515 ARG cc_start: 0.7102 (tpp80) cc_final: 0.6789 (tpt170)
REVERT: A 2531 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7149 (mt-10)
REVERT: A 2612 LYS cc_start: 0.7502 (ttpp) cc_final: 0.6962 (ttpt)
  outliers start: 19
  outliers final: 11
  residues processed: 81
  average time/residue: 1.0031
  time to fit residues: 84.4272
Evaluate side-chains
  77 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  401 LYS
Chi-restraints excluded: chain B residue  441 SER
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain A residue 2588 THR
Chi-restraints excluded: chain A residue 2600 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 27 optimal weight:    0.3980
   chunk 6 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 450 ASN
A2540 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4831 r_free = 0.4831 target = 0.243339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.212276 restraints weight = 4106.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.4568 rms_B_bonded: 2.06
r_work: 0.4434 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.4276 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.3646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4052  Z= 0.152
  Angle     :  0.648   7.508   5507  Z= 0.346
  Chirality :  0.050   0.202    563
  Planarity :  0.005   0.046    717
  Dihedral  :  6.485  55.807    544
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 26.56 %
    Favored  : 69.38 %
  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: -0.91 (0.40), residues: 492
  helix:  0.09 (0.94), residues: 36
  sheet: -1.47 (0.46), residues: 131
  loop : -0.22 (0.38), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 380 
 HIS   0.007   0.001   HIS B 296 
 PHE   0.007   0.001   PHE B 156 
 TYR   0.025   0.002   TYR B 485 
 ARG   0.007   0.001   ARG B 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03356 (  104)
  hydrogen bonds       : angle       6.42710 (  246)
  SS BOND              : bond        0.00177 (    5)
  SS BOND              : angle       0.85146 (   10)
  covalent geometry    : bond        0.00350 ( 4047)
  covalent geometry    : angle       0.64716 ( 5497)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: B  186 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7850 (mtp85)
REVERT: B  329 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7125 (pp20)
REVERT: B  401 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8311 (ttpp)
REVERT: B  488 MET cc_start: 0.7301 (mtp) cc_final: 0.6859 (mpp)
REVERT: A 2515 ARG cc_start: 0.6972 (tpp80) cc_final: 0.6670 (tpt170)
REVERT: A 2531 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7150 (mt-10)
REVERT: A 2612 LYS cc_start: 0.7508 (ttpp) cc_final: 0.6908 (ttpt)
  outliers start: 17
  outliers final: 12
  residues processed: 77
  average time/residue: 0.8672
  time to fit residues: 69.7948
Evaluate side-chains
  81 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  401 LYS
Chi-restraints excluded: chain B residue  441 SER
Chi-restraints excluded: chain B residue  456 ILE
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain A residue 2507 LEU
Chi-restraints excluded: chain A residue 2588 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    0.0470
   chunk 8 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0170
   chunk 44 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 26 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0370
   chunk 25 optimal weight:    0.5980
   chunk 36 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.2394

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

Flipped N/Q/H residues before XYZ refinement:
B 450 ASN
A2540 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.249709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.219930 restraints weight = 4101.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.4640 rms_B_bonded: 2.04
r_work: 0.4496 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4338 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   4052  Z= 0.108
  Angle     :  0.590   8.081   5507  Z= 0.315
  Chirality :  0.047   0.169    563
  Planarity :  0.005   0.049    717
  Dihedral  :  5.769  53.597    544
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 27.75 %
    Favored  : 69.38 %
  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: -0.70 (0.41), residues: 492
  helix:  0.36 (0.96), residues: 36
  sheet: -1.41 (0.47), residues: 118
  loop : -0.11 (0.38), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 454 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.006   0.001   PHE A2491 
 TYR   0.025   0.001   TYR B 485 
 ARG   0.008   0.000   ARG B 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02649 (  104)
  hydrogen bonds       : angle       6.00890 (  246)
  SS BOND              : bond        0.00109 (    5)
  SS BOND              : angle       0.63187 (   10)
  covalent geometry    : bond        0.00236 ( 4047)
  covalent geometry    : angle       0.58982 ( 5497)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3335.49 seconds
wall clock time: 58 minutes 21.21 seconds (3501.21 seconds total)