Starting phenix.real_space_refine
on Sun Apr 27 00:43:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ji0_36303/04_2025/8ji0_36303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ji0_36303/04_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_36303/04_2025/8ji0_36303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ji0_36303/04_2025/8ji0_36303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ji0_36303/04_2025/8ji0_36303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ji0_36303/04_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-5669/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: 3.85, per 1000 atoms: 0.98
  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: 1.01
  Conformation dependent library (CDL) restraints added in 481.3 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: 1.09
  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: 2.09

  Time building geometry restraints manager: 1.24 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:             41.250
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     18.730
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:30.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   91.180
-------------------------------------------------------------------------------
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  : 0.418 
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: 0.9743
  time to fit residues: 103.2932
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  : 0.421 
-------------------------------------------------------------------------------
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:    0.9990
   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 = 47)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.214543 restraints weight = 4128.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.4583 rms_B_bonded: 2.20
r_work: 0.4443 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.4443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
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  : 0.465 
Fit side-chains
   revert: symmetry clash
REVERT: B  210 MET cc_start: 0.7224 (mmm) cc_final: 0.6996 (mmt)
REVERT: B  329 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6807 (pp20)
REVERT: B  488 MET cc_start: 0.7296 (mtp) cc_final: 0.6632 (mpp)
REVERT: A 2515 ARG cc_start: 0.6859 (tpp80) cc_final: 0.6533 (tpt170)
REVERT: A 2612 LYS cc_start: 0.7384 (ttpp) cc_final: 0.7019 (ttpt)
REVERT: A 2613 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6796 (mt0)
  outliers start: 19
  outliers final: 8
  residues processed: 78
  average time/residue: 0.9067
  time to fit residues: 73.9907
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  : 0.467 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4868 r_free = 0.4868 target = 0.248015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.216945 restraints weight = 4129.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.4611 rms_B_bonded: 2.08
r_work: 0.4467 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.4307 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.4307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.2376

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= 0.130
  Angle     :  0.598   6.213   5507  Z= 0.319
  Chirality :  0.048   0.202    563
  Planarity :  0.005   0.048    717
  Dihedral  :  6.713  52.116    547
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 23.21 %
    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: -0.80 (0.40), residues: 492
  helix:  0.14 (0.95), residues: 36
  sheet: -1.53 (0.53), residues: 94
  loop : -0.28 (0.35), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   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   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03350 (  104)
  hydrogen bonds       : angle       6.32791 (  246)
  SS BOND              : bond        0.00192 (    5)
  SS BOND              : angle       0.81968 (   10)
  covalent geometry    : bond        0.00293 ( 4047)
  covalent geometry    : angle       0.59797 ( 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
  91 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: B  210 MET cc_start: 0.7402 (mmm) cc_final: 0.7194 (mmt)
REVERT: B  382 SER cc_start: 0.8809 (t) cc_final: 0.8599 (t)
REVERT: B  488 MET cc_start: 0.7302 (mtp) cc_final: 0.6544 (mpp)
REVERT: A 2515 ARG cc_start: 0.7012 (tpp80) cc_final: 0.6704 (tpt170)
REVERT: A 2612 LYS cc_start: 0.7552 (ttpp) cc_final: 0.7006 (ttpt)
  outliers start: 20
  outliers final: 7
  residues processed: 83
  average time/residue: 1.8603
  time to fit residues: 159.6995
Evaluate side-chains
  70 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 14 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.4830 r_free = 0.4830 target = 0.242345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.210523 restraints weight = 4233.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.4524 rms_B_bonded: 2.18
r_work: 0.4386 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.4221 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.4221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   4052  Z= 0.235
  Angle     :  0.704   7.336   5507  Z= 0.376
  Chirality :  0.052   0.182    563
  Planarity :  0.005   0.045    717
  Dihedral  :  7.104  56.313    545
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 24.88 %
    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: -1.17 (0.40), residues: 492
  helix: -0.38 (0.89), residues: 36
  sheet: -1.78 (0.42), residues: 143
  loop : -0.21 (0.38), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 380 
 HIS   0.005   0.001   HIS B 296 
 PHE   0.011   0.002   PHE A2521 
 TYR   0.023   0.002   TYR A2563 
 ARG   0.004   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04187 (  104)
  hydrogen bonds       : angle       6.75967 (  246)
  SS BOND              : bond        0.00340 (    5)
  SS BOND              : angle       1.34959 (   10)
  covalent geometry    : bond        0.00552 ( 4047)
  covalent geometry    : angle       0.70205 ( 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
  89 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: B  165 ARG cc_start: 0.7073 (mtt180) cc_final: 0.6743 (mtm180)
REVERT: B  329 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7093 (pp20)
REVERT: B  488 MET cc_start: 0.7337 (mtp) cc_final: 0.6793 (mpp)
REVERT: A 2515 ARG cc_start: 0.7017 (tpp80) cc_final: 0.6675 (tpt170)
REVERT: A 2612 LYS cc_start: 0.7581 (ttpp) cc_final: 0.7029 (ttpp)
  outliers start: 20
  outliers final: 11
  residues processed: 82
  average time/residue: 0.9424
  time to fit residues: 80.5671
Evaluate side-chains
  74 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
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  329 GLU
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  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:    0.0270
   chunk 2 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7038

-------------------------------------------------------------------------------
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 = 0.4844 r_free = 0.4844 target = 0.244206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.212218 restraints weight = 4237.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.4571 rms_B_bonded: 2.16
r_work: 0.4436 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.4278 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4052  Z= 0.144
  Angle     :  0.615   6.247   5507  Z= 0.326
  Chirality :  0.049   0.175    563
  Planarity :  0.005   0.043    717
  Dihedral  :  6.659  56.187    545
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 24.16 %
    Favored  : 71.05 %
  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: -0.08 (0.93), residues: 36
  sheet: -1.49 (0.45), residues: 131
  loop : -0.24 (0.37), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 168 
 HIS   0.005   0.001   HIS B 296 
 PHE   0.007   0.001   PHE A2533 
 TYR   0.018   0.002   TYR A2563 
 ARG   0.002   0.000   ARG B 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03398 (  104)
  hydrogen bonds       : angle       6.42038 (  246)
  SS BOND              : bond        0.00166 (    5)
  SS BOND              : angle       0.89631 (   10)
  covalent geometry    : bond        0.00331 ( 4047)
  covalent geometry    : angle       0.61435 ( 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
  89 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: B  329 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7065 (pp20)
REVERT: B  401 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8374 (ttpp)
REVERT: B  488 MET cc_start: 0.7165 (mtp) cc_final: 0.6776 (mpp)
REVERT: A 2515 ARG cc_start: 0.7016 (tpp80) cc_final: 0.6700 (tpt170)
REVERT: A 2531 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7109 (mt-10)
REVERT: A 2612 LYS cc_start: 0.7551 (ttpp) cc_final: 0.7005 (ttpt)
  outliers start: 20
  outliers final: 12
  residues processed: 80
  average time/residue: 0.8370
  time to fit residues: 70.0999
Evaluate side-chains
  75 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
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  434 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    0.2980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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
A2516 ASN
A2540 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4838 r_free = 0.4838 target = 0.243780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.212644 restraints weight = 4086.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.4595 rms_B_bonded: 2.05
r_work: 0.4451 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4293 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.4293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4052  Z= 0.142
  Angle     :  0.617   6.087   5507  Z= 0.326
  Chirality :  0.049   0.178    563
  Planarity :  0.005   0.043    717
  Dihedral  :  6.601  57.938    545
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 23.68 %
    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: -0.89 (0.40), residues: 492
  helix: -0.09 (0.93), residues: 36
  sheet: -1.50 (0.45), residues: 131
  loop : -0.15 (0.38), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 168 
 HIS   0.006   0.001   HIS B 296 
 PHE   0.006   0.001   PHE A2521 
 TYR   0.028   0.002   TYR A2563 
 ARG   0.002   0.000   ARG B 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03279 (  104)
  hydrogen bonds       : angle       6.33752 (  246)
  SS BOND              : bond        0.00178 (    5)
  SS BOND              : angle       0.87240 (   10)
  covalent geometry    : bond        0.00326 ( 4047)
  covalent geometry    : angle       0.61653 ( 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
  94 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: B  164 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.5916 (pp30)
REVERT: B  186 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7885 (mtp85)
REVERT: B  329 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7068 (pp20)
REVERT: B  488 MET cc_start: 0.7215 (mtp) cc_final: 0.6787 (mpp)
REVERT: A 2466 PHE cc_start: 0.6516 (t80) cc_final: 0.6304 (t80)
REVERT: A 2515 ARG cc_start: 0.7021 (tpp80) cc_final: 0.6707 (tpt170)
REVERT: A 2531 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7070 (mt-10)
REVERT: A 2612 LYS cc_start: 0.7541 (ttpp) cc_final: 0.6985 (ttpt)
  outliers start: 24
  outliers final: 12
  residues processed: 85
  average time/residue: 0.9024
  time to fit residues: 80.0755
Evaluate side-chains
  80 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
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  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 2507 LEU
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:    0.0970
   chunk 13 optimal weight:    0.1980
   chunk 19 optimal weight:    0.8980
   chunk 21 optimal weight:    0.3980
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0030
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.2788

-------------------------------------------------------------------------------
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
A2546 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.249296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.219079 restraints weight = 4127.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.4627 rms_B_bonded: 2.06
r_work: 0.4482 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4323 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4052  Z= 0.104
  Angle     :  0.581   7.704   5507  Z= 0.306
  Chirality :  0.047   0.180    563
  Planarity :  0.005   0.045    717
  Dihedral  :  5.950  54.850    545
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 25.84 %
    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: -0.56 (0.41), residues: 492
  helix:  0.51 (0.98), residues: 36
  sheet: -1.37 (0.47), residues: 118
  loop :  0.01 (0.38), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 168 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.005   0.001   PHE B 429 
 TYR   0.020   0.001   TYR B 485 
 ARG   0.003   0.000   ARG B 186 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02726 (  104)
  hydrogen bonds       : angle       6.02341 (  246)
  SS BOND              : bond        0.00081 (    5)
  SS BOND              : angle       0.61352 (   10)
  covalent geometry    : bond        0.00228 ( 4047)
  covalent geometry    : angle       0.58062 ( 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
  86 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: B  488 MET cc_start: 0.7265 (mtp) cc_final: 0.6875 (mpp)
REVERT: A 2515 ARG cc_start: 0.6978 (tpp80) cc_final: 0.6684 (tpt170)
REVERT: A 2531 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7075 (mt-10)
REVERT: A 2612 LYS cc_start: 0.7524 (ttpp) cc_final: 0.6978 (ttpt)
  outliers start: 16
  outliers final: 9
  residues processed: 80
  average time/residue: 0.8618
  time to fit residues: 71.9172
Evaluate side-chains
  74 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
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  304 ASN
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  441 SER
Chi-restraints excluded: chain B residue  459 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0070
   chunk 46 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.6398

-------------------------------------------------------------------------------
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 = 0.4849 r_free = 0.4849 target = 0.245318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.214510 restraints weight = 4079.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.4588 rms_B_bonded: 2.06
r_work: 0.4464 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.4298 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.3495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4052  Z= 0.142
  Angle     :  0.632  10.470   5507  Z= 0.331
  Chirality :  0.049   0.172    563
  Planarity :  0.005   0.045    717
  Dihedral  :  6.170  57.560    545
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 25.12 %
    Favored  : 70.10 %
  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: -0.67 (0.41), residues: 492
  helix:  0.35 (0.98), residues: 36
  sheet: -1.41 (0.46), residues: 131
  loop : -0.01 (0.38), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   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   0.004   0.000   ARG B 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03111 (  104)
  hydrogen bonds       : angle       6.18938 (  246)
  SS BOND              : bond        0.00166 (    5)
  SS BOND              : angle       0.80175 (   10)
  covalent geometry    : bond        0.00324 ( 4047)
  covalent geometry    : angle       0.63177 ( 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
  90 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
REVERT: B  186 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7816 (mtp85)
REVERT: B  467 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.5704 (tmmt)
REVERT: B  488 MET cc_start: 0.7333 (mtp) cc_final: 0.6878 (mpp)
REVERT: A 2515 ARG cc_start: 0.7068 (tpp80) cc_final: 0.6749 (tpt170)
REVERT: A 2531 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6991 (mt-10)
REVERT: A 2612 LYS cc_start: 0.7516 (ttpp) cc_final: 0.6964 (ttpt)
  outliers start: 20
  outliers final: 9
  residues processed: 85
  average time/residue: 0.9207
  time to fit residues: 81.8576
Evaluate side-chains
  78 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
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  287 THR
Chi-restraints excluded: chain B residue  304 ASN
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  441 SER
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  467 LYS
Chi-restraints excluded: chain A residue 2588 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0000
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4863 r_free = 0.4863 target = 0.247019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.216243 restraints weight = 4144.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.4602 rms_B_bonded: 2.09
r_work: 0.4455 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.4298 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.3586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4052  Z= 0.124
  Angle     :  0.617  10.292   5507  Z= 0.325
  Chirality :  0.048   0.175    563
  Planarity :  0.005   0.046    717
  Dihedral  :  6.041  57.757    545
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 27.51 %
    Favored  : 69.62 %
  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: -0.63 (0.41), residues: 492
  helix:  0.37 (0.97), residues: 36
  sheet: -1.37 (0.47), residues: 118
  loop : -0.05 (0.37), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 168 
 HIS   0.005   0.001   HIS B 296 
 PHE   0.005   0.001   PHE A2491 
 TYR   0.024   0.002   TYR B 485 
 ARG   0.006   0.000   ARG B 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02901 (  104)
  hydrogen bonds       : angle       6.11861 (  246)
  SS BOND              : bond        0.00109 (    5)
  SS BOND              : angle       0.66798 (   10)
  covalent geometry    : bond        0.00278 ( 4047)
  covalent geometry    : angle       0.61733 ( 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
  83 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: B  488 MET cc_start: 0.7313 (mtp) cc_final: 0.6860 (mpp)
REVERT: A 2515 ARG cc_start: 0.7060 (tpp80) cc_final: 0.6732 (tpt170)
REVERT: A 2531 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7016 (mt-10)
REVERT: A 2612 LYS cc_start: 0.7395 (ttpp) cc_final: 0.6856 (ttpt)
  outliers start: 12
  outliers final: 9
  residues processed: 78
  average time/residue: 0.8810
  time to fit residues: 71.7627
Evaluate side-chains
  77 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  441 SER
Chi-restraints excluded: chain B residue  456 ILE
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:    0.6980
   chunk 26 optimal weight:    0.4980
   chunk 0 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 450 ASN
** A2520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2540 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.245227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.214707 restraints weight = 4119.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.4588 rms_B_bonded: 2.07
r_work: 0.4437 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.4279 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.3620

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= 0.139
  Angle     :  0.626   7.127   5507  Z= 0.334
  Chirality :  0.049   0.171    563
  Planarity :  0.005   0.046    717
  Dihedral  :  5.860  57.730    542
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 27.03 %
    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: -0.69 (0.41), residues: 492
  helix:  0.31 (0.97), residues: 36
  sheet: -1.44 (0.45), residues: 131
  loop : -0.01 (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   0.026   0.002   TYR B 485 
 ARG   0.008   0.001   ARG B 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03080 (  104)
  hydrogen bonds       : angle       6.21112 (  246)
  SS BOND              : bond        0.00153 (    5)
  SS BOND              : angle       0.76384 (   10)
  covalent geometry    : bond        0.00317 ( 4047)
  covalent geometry    : angle       0.62596 ( 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
  84 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: B  186 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7829 (mtp85)
REVERT: B  488 MET cc_start: 0.7265 (mtp) cc_final: 0.6782 (mpp)
REVERT: A 2515 ARG cc_start: 0.6937 (tpp80) cc_final: 0.6629 (tpt170)
REVERT: A 2531 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7068 (mt-10)
REVERT: A 2612 LYS cc_start: 0.7525 (ttpp) cc_final: 0.6960 (ttpt)
  outliers start: 13
  outliers final: 9
  residues processed: 79
  average time/residue: 0.9685
  time to fit residues: 79.7215
Evaluate side-chains
  76 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
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  229 ASP
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  371 MET
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 SER
Chi-restraints excluded: chain B residue  441 SER
Chi-restraints excluded: chain B residue  456 ILE
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:    0.0670
   chunk 8 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0980
   chunk 5 optimal weight:    0.0170
   chunk 44 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0070
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.1574

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4906 r_free = 0.4906 target = 0.252290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.222705 restraints weight = 4127.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.4660 rms_B_bonded: 2.05
r_work: 0.4516 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.4359 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.3866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   4052  Z= 0.103
  Angle     :  0.597   8.993   5507  Z= 0.315
  Chirality :  0.047   0.178    563
  Planarity :  0.005   0.048    717
  Dihedral  :  5.607  59.558    542
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 27.51 %
    Favored  : 70.10 %
  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: -0.48 (0.41), residues: 492
  helix:  0.51 (0.98), residues: 36
  sheet: -1.30 (0.47), residues: 118
  loop :  0.06 (0.38), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 168 
 HIS   0.002   0.000   HIS B 296 
 PHE   0.006   0.001   PHE A2491 
 TYR   0.025   0.001   TYR B 485 
 ARG   0.006   0.000   ARG B 470 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02496 (  104)
  hydrogen bonds       : angle       5.86491 (  246)
  SS BOND              : bond        0.00083 (    5)
  SS BOND              : angle       0.56060 (   10)
  covalent geometry    : bond        0.00221 ( 4047)
  covalent geometry    : angle       0.59691 ( 5497)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3829.25 seconds
wall clock time: 67 minutes 6.85 seconds (4026.85 seconds total)