Starting phenix.real_space_refine
on Tue Feb 11 00:19:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e3b_30978/02_2025/7e3b_30978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e3b_30978/02_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_30978/02_2025/7e3b_30978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e3b_30978/02_2025/7e3b_30978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e3b_30978/02_2025/7e3b_30978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e3b_30978/02_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-5592/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: 3.02, per 1000 atoms: 0.92
  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: 0.66
  Conformation dependent library (CDL) restraints added in 426.6 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: 0.47
  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: 0.90

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 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:             1.390
  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:                     12.890
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.380
-------------------------------------------------------------------------------
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  : 0.357 
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: 0.1742
  time to fit residues: 17.8131
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  : 0.430 
-------------------------------------------------------------------------------
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 = 0.070954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.057528 restraints weight = 8684.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.059503 restraints weight = 4981.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.060876 restraints weight = 3431.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
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  29.163    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  : 0.394 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8483 (t70) cc_final: 0.8010 (p0)
REVERT: B    2 VAL cc_start: 0.9202 (t) cc_final: 0.8977 (t)
REVERT: B   53 TYR cc_start: 0.8673 (p90) cc_final: 0.8263 (p90)
REVERT: B  110 ASP cc_start: 0.8860 (t0) cc_final: 0.8630 (t0)
REVERT: C   24 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8290 (tm-30)
REVERT: C   79 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8629 (mm-40)
REVERT: C   82 ASP cc_start: 0.8826 (m-30) cc_final: 0.8624 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1721
  time to fit residues: 20.5373
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  : 0.363 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.2904 r_free = 0.2904 target = 0.070492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.057009 restraints weight = 8547.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.058910 restraints weight = 4950.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.060303 restraints weight = 3439.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   3385  Z= 0.339
  Angle     :  0.661  10.887   4610  Z= 0.350
  Chirality :  0.048   0.168    500
  Planarity :  0.004   0.035    594
  Dihedral  :  5.301  26.228    485
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  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: -1.66 (0.40), residues: 415
  helix: -2.42 (0.83), residues: 27
  sheet: -0.63 (0.47), residues: 130
  loop : -1.21 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  34 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.015   0.002   PHE A 429 
 TYR   0.016   0.002   TYR B  53 
 ARG   0.003   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  : 0.403 
Fit side-chains
REVERT: A  378 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8427 (tppt)
REVERT: A  467 ASP cc_start: 0.8510 (t70) cc_final: 0.7976 (p0)
REVERT: B    2 VAL cc_start: 0.9212 (t) cc_final: 0.8998 (t)
REVERT: B   48 ILE cc_start: 0.9618 (mt) cc_final: 0.9367 (mp)
REVERT: B   53 TYR cc_start: 0.8739 (p90) cc_final: 0.8354 (p90)
REVERT: C   24 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8206 (tm-30)
REVERT: C   36 TYR cc_start: 0.8994 (m-80) cc_final: 0.8368 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1727
  time to fit residues: 19.8717
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  : 0.362 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 18 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0670
   chunk 4 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.2950 r_free = 0.2950 target = 0.072836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.058929 restraints weight = 8425.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.061052 restraints weight = 4794.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.062526 restraints weight = 3268.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3385  Z= 0.228
  Angle     :  0.626  10.660   4610  Z= 0.326
  Chirality :  0.047   0.197    500
  Planarity :  0.004   0.034    594
  Dihedral  :  5.003  25.068    485
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.04
  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: -1.54 (0.40), residues: 415
  helix: -2.39 (0.86), residues: 27
  sheet: -0.53 (0.48), residues: 130
  loop : -1.13 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  34 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.023   0.001   PHE B  78 
 TYR   0.016   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  : 0.396 
Fit side-chains
REVERT: A  378 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8324 (tppt)
REVERT: A  452 LEU cc_start: 0.9513 (mt) cc_final: 0.9294 (mt)
REVERT: A  467 ASP cc_start: 0.8456 (t70) cc_final: 0.7945 (p0)
REVERT: B   48 ILE cc_start: 0.9600 (mt) cc_final: 0.9363 (mp)
REVERT: B   53 TYR cc_start: 0.8756 (p90) cc_final: 0.8414 (p90)
REVERT: B  110 ASP cc_start: 0.8807 (t70) cc_final: 0.8511 (t0)
REVERT: C   24 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8136 (tm-30)
REVERT: C   36 TYR cc_start: 0.8938 (m-10) cc_final: 0.8339 (m-80)
REVERT: C   88 CYS cc_start: 0.5878 (p) cc_final: 0.5546 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1559
  time to fit residues: 18.8924
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  : 0.413 
-------------------------------------------------------------------------------
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:    0.0060
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 38 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0980
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.3796

-------------------------------------------------------------------------------
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 = 0.2945 r_free = 0.2945 target = 0.072431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.059394 restraints weight = 8561.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.061409 restraints weight = 4877.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.062815 restraints weight = 3323.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.2040

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= 0.184
  Angle     :  0.602  10.353   4610  Z= 0.314
  Chirality :  0.047   0.217    500
  Planarity :  0.004   0.035    594
  Dihedral  :  4.781  23.305    485
  Min Nonbonded Distance : 2.550

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: -1.45 (0.40), residues: 415
  helix: -2.19 (0.92), residues: 27
  sheet: -0.47 (0.48), residues: 132
  loop : -1.08 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 112 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.017   0.001   PHE B  78 
 TYR   0.009   0.001   TYR B  53 
 ARG   0.004   0.001   ARG A 466 

*********************** 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
  100 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A  378 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8273 (tppt)
REVERT: A  452 LEU cc_start: 0.9491 (mt) cc_final: 0.9290 (mt)
REVERT: A  467 ASP cc_start: 0.8430 (t70) cc_final: 0.7881 (p0)
REVERT: B    2 VAL cc_start: 0.9145 (t) cc_final: 0.8879 (t)
REVERT: B   48 ILE cc_start: 0.9623 (mt) cc_final: 0.9365 (mp)
REVERT: B   53 TYR cc_start: 0.8645 (p90) cc_final: 0.8344 (p90)
REVERT: B  110 ASP cc_start: 0.8638 (t70) cc_final: 0.8399 (t0)
REVERT: C   24 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8140 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1645
  time to fit residues: 19.9634
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  : 0.432 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0170
   chunk 14 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.5218

-------------------------------------------------------------------------------
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 = 0.2946 r_free = 0.2946 target = 0.072667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.059542 restraints weight = 8845.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.061507 restraints weight = 4979.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.062886 restraints weight = 3399.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2209

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= 0.224
  Angle     :  0.631  10.221   4610  Z= 0.324
  Chirality :  0.047   0.231    500
  Planarity :  0.004   0.035    594
  Dihedral  :  4.761  22.227    485
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  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: -1.41 (0.40), residues: 415
  helix: -2.13 (0.94), residues: 27
  sheet: -0.45 (0.48), residues: 132
  loop : -1.06 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 112 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.020   0.001   PHE B  78 
 TYR   0.009   0.001   TYR B  53 
 ARG   0.004   0.001   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
  98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  378 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8302 (tppt)
REVERT: A  467 ASP cc_start: 0.8422 (t70) cc_final: 0.7889 (p0)
REVERT: B    2 VAL cc_start: 0.9135 (t) cc_final: 0.8881 (t)
REVERT: B   48 ILE cc_start: 0.9579 (mt) cc_final: 0.9357 (mp)
REVERT: B   53 TYR cc_start: 0.8592 (p90) cc_final: 0.8287 (p90)
REVERT: B   98 ASP cc_start: 0.8819 (t70) cc_final: 0.8503 (t0)
REVERT: C   23 CYS cc_start: 0.5235 (t) cc_final: 0.3996 (t)
REVERT: C   24 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8110 (tm-30)
REVERT: C   36 TYR cc_start: 0.8909 (m-10) cc_final: 0.8390 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1681
  time to fit residues: 19.7995
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  : 0.401 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 7 optimal weight:    0.4980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.2925 r_free = 0.2925 target = 0.071502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.058374 restraints weight = 8533.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.060376 restraints weight = 4894.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.061684 restraints weight = 3359.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3385  Z= 0.265
  Angle     :  0.659  10.067   4610  Z= 0.337
  Chirality :  0.048   0.247    500
  Planarity :  0.004   0.035    594
  Dihedral  :  4.844  23.233    485
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.04
  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: -1.42 (0.40), residues: 415
  helix: -2.29 (0.93), residues: 27
  sheet: -0.46 (0.48), residues: 132
  loop : -1.05 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 112 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.017   0.001   PHE B  78 
 TYR   0.020   0.001   TYR B  52 
 ARG   0.004   0.001   ARG A 466 

*********************** 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  : 0.595 
Fit side-chains
REVERT: A  378 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8214 (tppt)
REVERT: A  467 ASP cc_start: 0.8424 (t70) cc_final: 0.7861 (p0)
REVERT: B    2 VAL cc_start: 0.9124 (t) cc_final: 0.8854 (t)
REVERT: B   48 ILE cc_start: 0.9602 (mt) cc_final: 0.9351 (mp)
REVERT: C   24 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: C   36 TYR cc_start: 0.8973 (m-10) cc_final: 0.8442 (m-80)
REVERT: C   88 CYS cc_start: 0.5848 (p) cc_final: 0.5434 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1828
  time to fit residues: 20.6385
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  : 0.396 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 39 optimal weight:    0.1980
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    0.1980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.2952 r_free = 0.2952 target = 0.072924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.059687 restraints weight = 8519.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.061670 restraints weight = 4930.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.063000 restraints weight = 3387.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.2344

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= 0.210
  Angle     :  0.664   9.871   4610  Z= 0.337
  Chirality :  0.047   0.249    500
  Planarity :  0.004   0.034    594
  Dihedral  :  4.697  22.659    485
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  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: -1.27 (0.40), residues: 415
  helix: -2.31 (0.96), residues: 27
  sheet: -0.34 (0.48), residues: 132
  loop : -0.94 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 112 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.017   0.001   PHE B  78 
 TYR   0.025   0.001   TYR B  52 
 ARG   0.005   0.001   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
  94 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  378 LYS cc_start: 0.8409 (mmtt) cc_final: 0.8142 (tppt)
REVERT: A  452 LEU cc_start: 0.9456 (mt) cc_final: 0.9215 (mt)
REVERT: A  467 ASP cc_start: 0.8380 (t70) cc_final: 0.7840 (p0)
REVERT: A  472 ILE cc_start: 0.8630 (mm) cc_final: 0.8409 (tp)
REVERT: B    2 VAL cc_start: 0.9078 (t) cc_final: 0.8799 (t)
REVERT: B   48 ILE cc_start: 0.9570 (mt) cc_final: 0.9281 (mp)
REVERT: B   81 LYS cc_start: 0.9231 (mmtm) cc_final: 0.8982 (mptt)
REVERT: C   24 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8162 (tm-30)
REVERT: C   36 TYR cc_start: 0.8871 (m-10) cc_final: 0.8145 (m-80)
REVERT: C   61 ARG cc_start: 0.8414 (ptp90) cc_final: 0.8171 (ptp90)
REVERT: C   88 CYS cc_start: 0.5718 (p) cc_final: 0.5137 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1696
  time to fit residues: 19.0192
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  : 0.396 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0980
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0270
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 40 optimal weight:    0.3980
   chunk 2 optimal weight:    0.0370
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.2316

-------------------------------------------------------------------------------
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 = 0.2973 r_free = 0.2973 target = 0.074000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.060901 restraints weight = 8509.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.062788 restraints weight = 4908.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.064198 restraints weight = 3407.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2615

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= 0.169
  Angle     :  0.633   9.348   4610  Z= 0.320
  Chirality :  0.046   0.185    500
  Planarity :  0.004   0.034    594
  Dihedral  :  4.574  21.746    485
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  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: -1.10 (0.41), residues: 415
  helix: -2.34 (0.96), residues: 27
  sheet: -0.08 (0.50), residues: 132
  loop : -0.89 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 112 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.016   0.001   PHE B  78 
 TYR   0.024   0.001   TYR B  53 
 ARG   0.005   0.001   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
  99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8356 (mmtt) cc_final: 0.8079 (tppt)
REVERT: A  452 LEU cc_start: 0.9430 (mt) cc_final: 0.9178 (mt)
REVERT: A  467 ASP cc_start: 0.8378 (t70) cc_final: 0.7866 (p0)
REVERT: B    2 VAL cc_start: 0.9061 (t) cc_final: 0.8761 (t)
REVERT: B   53 TYR cc_start: 0.8716 (p90) cc_final: 0.8310 (p90)
REVERT: B   82 LEU cc_start: 0.9088 (tp) cc_final: 0.8869 (tp)
REVERT: B  120 VAL cc_start: 0.7895 (p) cc_final: 0.7321 (p)
REVERT: C   24 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: C   36 TYR cc_start: 0.8937 (m-10) cc_final: 0.8292 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1962
  time to fit residues: 23.0371
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  : 0.387 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.2945 r_free = 0.2945 target = 0.072545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.059104 restraints weight = 8554.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.061069 restraints weight = 5008.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.062326 restraints weight = 3487.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   3385  Z= 0.328
  Angle     :  0.696   9.123   4610  Z= 0.356
  Chirality :  0.049   0.268    500
  Planarity :  0.005   0.035    594
  Dihedral  :  4.718  24.304    485
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  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: -1.22 (0.41), residues: 415
  helix: -2.35 (0.95), residues: 27
  sheet: -0.29 (0.48), residues: 132
  loop : -0.90 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 112 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.013   0.001   PHE B  78 
 TYR   0.023   0.002   TYR B  53 
 ARG   0.010   0.001   ARG B  97 

********************** 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
  91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  378 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8072 (tppt)
REVERT: A  467 ASP cc_start: 0.8393 (t70) cc_final: 0.7839 (p0)
REVERT: B    2 VAL cc_start: 0.9090 (t) cc_final: 0.8799 (t)
REVERT: B   81 LYS cc_start: 0.9302 (mmtm) cc_final: 0.9091 (mptt)
REVERT: C    4 MET cc_start: 0.7757 (mmp) cc_final: 0.7517 (mmp)
REVERT: C   24 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8120 (tm-30)
REVERT: C   88 CYS cc_start: 0.5918 (p) cc_final: 0.5404 (p)
REVERT: C   93 ASN cc_start: 0.8339 (t0) cc_final: 0.7916 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.1617
  time to fit residues: 17.8124
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  : 0.420 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 14 optimal weight:    0.1980
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 23 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0040
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
B  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.073544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.060286 restraints weight = 8622.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.062254 restraints weight = 4998.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.063520 restraints weight = 3449.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3385  Z= 0.220
  Angle     :  0.668   9.255   4610  Z= 0.337
  Chirality :  0.048   0.277    500
  Planarity :  0.004   0.034    594
  Dihedral  :  4.675  22.928    485
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.33
  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: -1.16 (0.41), residues: 415
  helix: -2.40 (0.90), residues: 27
  sheet: -0.17 (0.49), residues: 132
  loop : -0.90 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 112 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.011   0.001   PHE B  78 
 TYR   0.020   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: 1607.16 seconds
wall clock time: 29 minutes 34.62 seconds (1774.62 seconds total)