Starting phenix.real_space_refine
on Wed Mar  5 19:21:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e3b_30978/03_2025/7e3b_30978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e3b_30978/03_2025/7e3b_30978.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e3b_30978/03_2025/7e3b_30978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e3b_30978/03_2025/7e3b_30978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e3b_30978/03_2025/7e3b_30978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e3b_30978/03_2025/7e3b_30978.cif"
  }
  resolution = 4.2
  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=   0.000 sd=   0.001
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      14      5.16       5
     C    2095      2.51       5
     N     541      2.21       5
     O     649      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3299
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "B"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 941
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    Chain: "C"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 808
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.15, per 1000 atoms: 0.95
  Number of scatterers: 3299
  At special positions: 0
  Unit cell: (68.481, 85.873, 72.829, 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      14     16.00
     O     649      8.00
     N     541      7.00
     C    2095      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 343 "
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 405.8 milliseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  770

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 9 sheets defined
      11.6% alpha, 29.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 4.331A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.364A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.136A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'B' and resid 61 through 64
    Processing helix  chain 'B' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.561A  pdb=" N   SER B  35 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 11
    Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11
      removed outlier: 3.918A  pdb=" N   THR C  97 " --> pdb=" O   GLN C  90 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 49

    111 hydrogen bonds defined for protein.
    255 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: 0.89

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1049
        1.35 -     1.48: 968
        1.48 -     1.60: 1352
        1.60 -     1.73: 0
        1.73 -     1.85: 16
  Bond restraints: 3385
  Sorted by residual:
  bond pdb=" CB  PHE B  78 "
       pdb=" CG  PHE B  78 "
    ideal  model  delta    sigma   weight residual
    1.502  1.454  0.048 2.30e-02 1.89e+03 4.40e+00
  bond pdb=" N   TRP B 112 "
       pdb=" CA  TRP B 112 "
    ideal  model  delta    sigma   weight residual
    1.457  1.479 -0.022 1.29e-02 6.01e+03 2.88e+00
  bond pdb=" CD2 PHE B  78 "
       pdb=" CE2 PHE B  78 "
    ideal  model  delta    sigma   weight residual
    1.382  1.338  0.044 3.00e-02 1.11e+03 2.14e+00
  bond pdb=" CB  TRP B 112 "
       pdb=" CG  TRP B 112 "
    ideal  model  delta    sigma   weight residual
    1.498  1.453  0.045 3.10e-02 1.04e+03 2.12e+00
  bond pdb=" CB  CYS A 379 "
       pdb=" SG  CYS A 379 "
    ideal  model  delta    sigma   weight residual
    1.808  1.854 -0.046 3.30e-02 9.18e+02 1.97e+00
  ... (remaining 3380 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 4473
        2.09 -     4.17: 117
        4.17 -     6.26: 17
        6.26 -     8.35: 2
        8.35 -    10.44: 1
  Bond angle restraints: 4610
  Sorted by residual:
  angle pdb=" CA  CYS A 432 "
        pdb=" CB  CYS A 432 "
        pdb=" SG  CYS A 432 "
      ideal   model   delta    sigma   weight residual
     114.40  124.84  -10.44 2.30e+00 1.89e-01 2.06e+01
  angle pdb=" CB  LYS B  13 "
        pdb=" CG  LYS B  13 "
        pdb=" CD  LYS B  13 "
      ideal   model   delta    sigma   weight residual
     111.30  118.65   -7.35 2.30e+00 1.89e-01 1.02e+01
  angle pdb=" C   ILE C  83 "
        pdb=" N   ALA C  84 "
        pdb=" CA  ALA C  84 "
      ideal   model   delta    sigma   weight residual
     122.09  116.48    5.61 1.86e+00 2.89e-01 9.11e+00
  angle pdb=" N   CYS A 432 "
        pdb=" CA  CYS A 432 "
        pdb=" C   CYS A 432 "
      ideal   model   delta    sigma   weight residual
     108.60  112.87   -4.27 1.46e+00 4.69e-01 8.54e+00
  angle pdb=" C   GLY A 431 "
        pdb=" N   CYS A 432 "
        pdb=" CA  CYS A 432 "
      ideal   model   delta    sigma   weight residual
     121.80  116.95    4.85 1.71e+00 3.42e-01 8.04e+00
  ... (remaining 4605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 1814
       17.19 -    34.37: 147
       34.37 -    51.55: 26
       51.55 -    68.74: 7
       68.74 -    85.92: 3
  Dihedral angle restraints: 1997
    sinusoidal: 779
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.09   55.91     1      1.00e+01 1.00e-02 4.22e+01
  dihedral pdb=" CA  CYS A 432 "
           pdb=" C   CYS A 432 "
           pdb=" N   VAL A 433 "
           pdb=" CA  VAL A 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.54  -25.46     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ASP B 110 "
           pdb=" C   ASP B 110 "
           pdb=" N   ILE B 111 "
           pdb=" CA  ILE B 111 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.89  -21.11     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 1994 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 280
       0.033 -    0.066: 146
       0.066 -    0.099: 41
       0.099 -    0.132: 23
       0.132 -    0.165: 10
  Chirality restraints: 500
  Sorted by residual:
  chirality pdb=" CA  ILE C  29 "
            pdb=" N   ILE C  29 "
            pdb=" C   ILE C  29 "
            pdb=" CB  ILE C  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.81e-01
  chirality pdb=" CA  CYS A 432 "
            pdb=" N   CYS A 432 "
            pdb=" C   CYS A 432 "
            pdb=" CB  CYS A 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.56e-01
  chirality pdb=" CB  ILE B 111 "
            pdb=" CA  ILE B 111 "
            pdb=" CG1 ILE B 111 "
            pdb=" CG2 ILE B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.92e-01
  ... (remaining 497 not shown)

  Planarity restraints: 595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  34 "   -0.025 2.00e-02 2.50e+03   1.61e-02 6.50e+00
        pdb=" CG  TRP B  34 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  34 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  34 "    0.008 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  34 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  34 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  34 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  34 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B   8 "    0.027 5.00e-02 4.00e+02   4.06e-02 2.63e+00
        pdb=" N   PRO B   9 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B   9 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B   9 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  78 "    0.008 2.00e-02 2.50e+03   1.55e-02 2.40e+00
        pdb=" C   PHE B  78 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   PHE B  78 "    0.010 2.00e-02 2.50e+03
        pdb=" N   SER B  79 "    0.009 2.00e-02 2.50e+03
  ... (remaining 592 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 746
        2.77 -     3.30: 3195
        3.30 -     3.84: 5475
        3.84 -     4.37: 6437
        4.37 -     4.90: 11064
  Nonbonded interactions: 26917
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  98 "
            pdb=" N   ARG B  99 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" NH2 ARG A 346 "
            pdb=" OD2 ASP B  98 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" OD1 ASN A 450 "
            pdb=" OH  TYR B  50 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" NH2 ARG A 454 "
            pdb=" O   SER A 469 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" NH1 ARG C  18 "
            pdb=" OG1 THR C  20 "
     model   vdw
     2.296 3.120
  ... (remaining 26912 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  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:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.660
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
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      :  0.006   0.048   3385  Z= 0.400
  Angle     :  0.810  10.437   4610  Z= 0.459
  Chirality :  0.049   0.165    500
  Planarity :  0.004   0.041    594
  Dihedral  : 13.333  85.922   1209
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 16.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.38), residues: 415
  helix: -3.08 (0.86), residues: 26
  sheet: -1.07 (0.45), residues: 130
  loop : -1.32 (0.35), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP B  34 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.019   0.002   PHE B  78 
 TYR   0.022   0.002   TYR A 365 
 ARG   0.006   0.001   ARG C  61 

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8499 (t70) cc_final: 0.8014 (p0)
REVERT: B   89 ASP cc_start: 0.9199 (m-30) cc_final: 0.8902 (m-30)
REVERT: B  110 ASP cc_start: 0.8840 (t0) cc_final: 0.8568 (t0)
REVERT: C   83 ILE cc_start: 0.9384 (mt) cc_final: 0.9178 (tt)
REVERT: C   88 CYS cc_start: 0.6457 (p) cc_final: 0.6036 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.2287
  time to fit residues: 24.0241
Evaluate side-chains
  76 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0970
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0070
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.070955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.057528 restraints weight = 8684.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.059505 restraints weight = 4980.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.060782 restraints weight = 3430.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3385  Z= 0.245
  Angle     :  0.633  10.254   4610  Z= 0.337
  Chirality :  0.047   0.162    500
  Planarity :  0.004   0.033    594
  Dihedral  :  5.544  29.164    485
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.62 (0.40), residues: 415
  helix: -2.25 (0.87), residues: 27
  sheet: -0.65 (0.47), residues: 130
  loop : -1.17 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  34 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.015   0.001   PHE B  78 
 TYR   0.022   0.002   TYR B  53 
 ARG   0.003   0.001   ARG B  64 

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8481 (t70) cc_final: 0.8007 (p0)
REVERT: B    2 VAL cc_start: 0.9203 (t) cc_final: 0.8979 (t)
REVERT: B   53 TYR cc_start: 0.8674 (p90) cc_final: 0.8265 (p90)
REVERT: B  110 ASP cc_start: 0.8861 (t0) cc_final: 0.8633 (t0)
REVERT: C   24 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8283 (tm-30)
REVERT: C   79 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8628 (mm-40)
REVERT: C   82 ASP cc_start: 0.8821 (m-30) cc_final: 0.8619 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1598
  time to fit residues: 19.1808
Evaluate side-chains
  84 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.9184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.070446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.057036 restraints weight = 8555.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.058966 restraints weight = 5013.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.060296 restraints weight = 3486.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3385  Z= 0.342
  Angle     :  0.662  10.872   4610  Z= 0.350
  Chirality :  0.048   0.169    500
  Planarity :  0.004   0.035    594
  Dihedral  :  5.306  26.304    485
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.68 (0.40), residues: 415
  helix: -2.41 (0.84), residues: 27
  sheet: -0.72 (0.47), residues: 132
  loop : -1.17 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  34 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.016   0.002   PHE B  78 
 TYR   0.017   0.002   TYR B  53 
 ARG   0.004   0.001   ARG C  61 

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A  378 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8442 (tppt)
REVERT: A  467 ASP cc_start: 0.8525 (t70) cc_final: 0.7990 (p0)
REVERT: B    2 VAL cc_start: 0.9207 (t) cc_final: 0.8991 (t)
REVERT: B   48 ILE cc_start: 0.9624 (mt) cc_final: 0.9388 (mp)
REVERT: B   53 TYR cc_start: 0.8724 (p90) cc_final: 0.8327 (p90)
REVERT: B  110 ASP cc_start: 0.8886 (t0) cc_final: 0.8669 (t0)
REVERT: C   24 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8214 (tm-30)
REVERT: C   36 TYR cc_start: 0.9003 (m-80) cc_final: 0.8354 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1718
  time to fit residues: 19.7732
Evaluate side-chains
  82 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0040
   chunk 4 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.5592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.072770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.059228 restraints weight = 8432.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.061244 restraints weight = 4952.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.062562 restraints weight = 3444.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3385  Z= 0.230
  Angle     :  0.625  10.736   4610  Z= 0.326
  Chirality :  0.047   0.206    500
  Planarity :  0.004   0.034    594
  Dihedral  :  5.031  24.974    485
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.56 (0.40), residues: 415
  helix: -2.37 (0.86), residues: 27
  sheet: -0.55 (0.48), residues: 130
  loop : -1.15 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  34 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.023   0.002   PHE B  78 
 TYR   0.017   0.001   TYR B  52 
 ARG   0.003   0.000   ARG C  61 

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A  378 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8331 (tppt)
REVERT: A  452 LEU cc_start: 0.9507 (mt) cc_final: 0.9285 (mt)
REVERT: A  467 ASP cc_start: 0.8476 (t70) cc_final: 0.7965 (p0)
REVERT: B   48 ILE cc_start: 0.9617 (mt) cc_final: 0.9392 (mp)
REVERT: C   24 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8164 (tm-30)
REVERT: C   36 TYR cc_start: 0.8947 (m-80) cc_final: 0.8304 (m-80)
REVERT: C   88 CYS cc_start: 0.5861 (p) cc_final: 0.5526 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1551
  time to fit residues: 18.7562
Evaluate side-chains
  83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0970
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.072155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.058996 restraints weight = 8612.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.060994 restraints weight = 4909.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.062453 restraints weight = 3362.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3385  Z= 0.223
  Angle     :  0.623  10.490   4610  Z= 0.324
  Chirality :  0.047   0.233    500
  Planarity :  0.004   0.035    594
  Dihedral  :  4.848  23.161    485
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.50 (0.40), residues: 415
  helix: -2.26 (0.91), residues: 27
  sheet: -0.54 (0.48), residues: 132
  loop : -1.10 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 105 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.018   0.001   PHE B  78 
 TYR   0.016   0.001   TYR B  52 
 ARG   0.004   0.001   ARG C  61 

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  378 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8319 (tppt)
REVERT: A  452 LEU cc_start: 0.9482 (mt) cc_final: 0.9278 (mt)
REVERT: A  467 ASP cc_start: 0.8440 (t70) cc_final: 0.7885 (p0)
REVERT: B    2 VAL cc_start: 0.9146 (t) cc_final: 0.8892 (t)
REVERT: B   48 ILE cc_start: 0.9616 (mt) cc_final: 0.9365 (mp)
REVERT: B   53 TYR cc_start: 0.8770 (p90) cc_final: 0.8509 (p90)
REVERT: C   24 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: C   93 ASN cc_start: 0.8261 (t0) cc_final: 0.7941 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1503
  time to fit residues: 17.6447
Evaluate side-chains
  79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    0.3980
   chunk 23 optimal weight:    0.0870
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.071695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.058482 restraints weight = 8844.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.060559 restraints weight = 4967.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.061976 restraints weight = 3361.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3385  Z= 0.254
  Angle     :  0.641  10.355   4610  Z= 0.331
  Chirality :  0.047   0.229    500
  Planarity :  0.004   0.035    594
  Dihedral  :  4.872  23.052    485
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.51 (0.40), residues: 415
  helix: -2.23 (0.92), residues: 27
  sheet: -0.52 (0.48), residues: 132
  loop : -1.12 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 105 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.020   0.001   PHE B  78 
 TYR   0.015   0.001   TYR B  52 
 ARG   0.003   0.000   ARG A 466 

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8306 (tppt)
REVERT: A  467 ASP cc_start: 0.8432 (t70) cc_final: 0.7882 (p0)
REVERT: B    2 VAL cc_start: 0.9120 (t) cc_final: 0.8857 (t)
REVERT: B   48 ILE cc_start: 0.9580 (mt) cc_final: 0.9330 (mp)
REVERT: B   98 ASP cc_start: 0.8829 (t70) cc_final: 0.8550 (t0)
REVERT: C   23 CYS cc_start: 0.5272 (t) cc_final: 0.4012 (t)
REVERT: C   24 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8098 (tm-30)
REVERT: C   93 ASN cc_start: 0.8258 (t0) cc_final: 0.7928 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1617
  time to fit residues: 18.8734
Evaluate side-chains
  83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.9380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.070436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.057274 restraints weight = 8571.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.059143 restraints weight = 5002.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.060513 restraints weight = 3486.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   3385  Z= 0.342
  Angle     :  0.698  10.539   4610  Z= 0.360
  Chirality :  0.049   0.252    500
  Planarity :  0.004   0.035    594
  Dihedral  :  5.035  24.210    485
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.60 (0.39), residues: 415
  helix: -2.43 (0.93), residues: 27
  sheet: -0.62 (0.47), residues: 132
  loop : -1.14 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B  34 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.018   0.002   PHE B  78 
 TYR   0.027   0.002   TYR B  52 
 ARG   0.004   0.001   ARG C  61 

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A  378 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8300 (tppt)
REVERT: A  467 ASP cc_start: 0.8431 (t70) cc_final: 0.7877 (p0)
REVERT: B    2 VAL cc_start: 0.9128 (t) cc_final: 0.8862 (t)
REVERT: B   48 ILE cc_start: 0.9578 (mt) cc_final: 0.9317 (mp)
REVERT: C   24 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8060 (tm-30)
REVERT: C   61 ARG cc_start: 0.8370 (ptp90) cc_final: 0.7948 (ptp90)
REVERT: C   88 CYS cc_start: 0.6004 (p) cc_final: 0.5738 (p)
REVERT: C   93 ASN cc_start: 0.8319 (t0) cc_final: 0.7954 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1640
  time to fit residues: 18.2384
Evaluate side-chains
  83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0570
   chunk 39 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.5498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.071550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.058242 restraints weight = 8570.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.060219 restraints weight = 4905.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.061596 restraints weight = 3365.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3385  Z= 0.231
  Angle     :  0.667  10.302   4610  Z= 0.340
  Chirality :  0.048   0.250    500
  Planarity :  0.004   0.034    594
  Dihedral  :  4.871  23.114    485
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.42 (0.40), residues: 415
  helix: -2.24 (0.99), residues: 27
  sheet: -0.49 (0.47), residues: 132
  loop : -1.02 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 105 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.016   0.001   PHE B  78 
 TYR   0.024   0.001   TYR B  53 
 ARG   0.004   0.000   ARG A 466 

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8234 (tppt)
REVERT: A  452 LEU cc_start: 0.9483 (mt) cc_final: 0.9242 (mt)
REVERT: A  467 ASP cc_start: 0.8419 (t70) cc_final: 0.7869 (p0)
REVERT: B    2 VAL cc_start: 0.9089 (t) cc_final: 0.8822 (t)
REVERT: B   48 ILE cc_start: 0.9572 (mt) cc_final: 0.9305 (mp)
REVERT: B   53 TYR cc_start: 0.8800 (p90) cc_final: 0.8357 (p90)
REVERT: C   24 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8135 (tm-30)
REVERT: C   36 TYR cc_start: 0.8909 (m-10) cc_final: 0.8349 (m-80)
REVERT: C   88 CYS cc_start: 0.5933 (p) cc_final: 0.5321 (p)
REVERT: C   93 ASN cc_start: 0.8239 (t0) cc_final: 0.7957 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.2104
  time to fit residues: 23.6510
Evaluate side-chains
  79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    0.2980
   chunk 7 optimal weight:    0.0040
   chunk 22 optimal weight:    0.9980
   chunk 36 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.3992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.072545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.059295 restraints weight = 8608.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.061302 restraints weight = 4918.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.062669 restraints weight = 3365.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3385  Z= 0.199
  Angle     :  0.644  10.048   4610  Z= 0.329
  Chirality :  0.047   0.173    500
  Planarity :  0.004   0.034    594
  Dihedral  :  4.683  22.509    485
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.26 (0.41), residues: 415
  helix: -2.06 (1.01), residues: 27
  sheet: -0.32 (0.48), residues: 132
  loop : -0.96 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 112 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.016   0.001   PHE B  78 
 TYR   0.019   0.001   TYR B  53 
 ARG   0.005   0.000   ARG A 466 

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8236 (tppt)
REVERT: A  452 LEU cc_start: 0.9464 (mt) cc_final: 0.9214 (mt)
REVERT: A  467 ASP cc_start: 0.8405 (t70) cc_final: 0.7860 (p0)
REVERT: B    2 VAL cc_start: 0.9070 (t) cc_final: 0.8783 (t)
REVERT: B   48 ILE cc_start: 0.9562 (mt) cc_final: 0.9242 (mp)
REVERT: B   53 TYR cc_start: 0.8708 (p90) cc_final: 0.8375 (p90)
REVERT: C   24 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8149 (tm-30)
REVERT: C   36 TYR cc_start: 0.8833 (m-10) cc_final: 0.8280 (m-80)
REVERT: C   93 ASN cc_start: 0.8216 (t0) cc_final: 0.7953 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1809
  time to fit residues: 20.7443
Evaluate side-chains
  83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0270
   overall best weight:    0.5238

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.072722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.058971 restraints weight = 8520.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.061055 restraints weight = 4818.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.062478 restraints weight = 3284.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3385  Z= 0.234
  Angle     :  0.686   9.533   4610  Z= 0.349
  Chirality :  0.049   0.271    500
  Planarity :  0.004   0.034    594
  Dihedral  :  4.741  23.371    485
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.24 (0.41), residues: 415
  helix: -2.20 (0.95), residues: 27
  sheet: -0.31 (0.49), residues: 132
  loop : -0.94 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 112 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.017   0.001   PHE B  78 
 TYR   0.019   0.001   TYR B  53 
 ARG   0.005   0.001   ARG A 466 

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8368 (t70) cc_final: 0.7817 (p0)
REVERT: B    2 VAL cc_start: 0.9064 (t) cc_final: 0.8801 (t)
REVERT: B   48 ILE cc_start: 0.9528 (mt) cc_final: 0.9313 (mt)
REVERT: B   53 TYR cc_start: 0.8715 (p90) cc_final: 0.8394 (p90)
REVERT: C   24 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8100 (tm-30)
REVERT: C   36 TYR cc_start: 0.8852 (m-10) cc_final: 0.8250 (m-80)
REVERT: C   88 CYS cc_start: 0.5928 (p) cc_final: 0.5307 (p)
REVERT: C   93 ASN cc_start: 0.8280 (t0) cc_final: 0.7967 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1551
  time to fit residues: 17.5357
Evaluate side-chains
  82 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 14 optimal weight:    0.4980
   chunk 9 optimal weight:    0.0570
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.4898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.072775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.059185 restraints weight = 8650.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.061194 restraints weight = 4865.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.062598 restraints weight = 3322.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3385  Z= 0.224
  Angle     :  0.657   9.042   4610  Z= 0.337
  Chirality :  0.048   0.269    500
  Planarity :  0.004   0.034    594
  Dihedral  :  4.697  23.806    485
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.15 (0.41), residues: 415
  helix: -2.14 (0.94), residues: 27
  sheet: -0.18 (0.49), residues: 132
  loop : -0.91 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 112 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.018   0.001   PHE B  78 
 TYR   0.018   0.001   TYR B  53 
 ARG   0.005   0.001   ARG A 466 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1657.58 seconds
wall clock time: 29 minutes 34.96 seconds (1774.96 seconds total)