Starting phenix.real_space_refine
on Thu Jul 24 01:39:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5b_44206/07_2025/9b5b_44206.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5b_44206/07_2025/9b5b_44206.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5b_44206/07_2025/9b5b_44206.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5b_44206/07_2025/9b5b_44206.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5b_44206/07_2025/9b5b_44206.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5b_44206/07_2025/9b5b_44206.cif"
  }
  resolution = 3.31
  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=   0.044
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    3110      2.51       5
     N     824      2.21       5
     O     923      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4871
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1162
          Classifications: {'peptide': 147}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
    Chain: "B"
      Number of atoms: 596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 596
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 3107
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 377, 3099
          Classifications: {'peptide': 377}
          Link IDs: {'PTRANS': 14, 'TRANS': 362}
      Conformer: "B"
        Number of residues, atoms: 377, 3099
          Classifications: {'peptide': 377}
          Link IDs: {'PTRANS': 14, 'TRANS': 362}
          bond proxies already assigned to first conformer: 3161
    Chain: "B"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'A1AIV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.74, per 1000 atoms: 1.18
  Number of scatterers: 4871
  At special positions: 0
  Unit cell: (74.48, 82.992, 98.952, 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     923      8.00
     N     824      7.00
     C    3110      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 6 sheets defined
      48.2% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 16
    Processing helix  chain 'A' and resid 98 through 110
      removed outlier: 3.690A  pdb=" N   VAL A 102 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 130
    Processing helix  chain 'A' and resid 130 through 146
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 56 through 60
    Processing helix  chain 'C' and resid 293 through 306
    Processing helix  chain 'C' and resid 307 through 311
      removed outlier: 4.119A  pdb=" N   ALA C 311 " --> pdb=" O   PRO C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 335
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 357 through 374
    Processing helix  chain 'C' and resid 375 through 379
    Processing helix  chain 'C' and resid 395 through 400
    Processing helix  chain 'C' and resid 402 through 420
      removed outlier: 4.489A  pdb=" N   TYR C 406 " --> pdb=" O   ASP C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 437
      removed outlier: 3.516A  pdb=" N   TYR C 433 " --> pdb=" O   VAL C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 449
    Processing helix  chain 'C' and resid 450 through 463
    Processing helix  chain 'C' and resid 491 through 495
      removed outlier: 3.807A  pdb=" N   ASN C 494 " --> pdb=" O   ASN C 491 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE C 495 " --> pdb=" O   GLY C 492 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 491 through 495'
    Processing helix  chain 'C' and resid 501 through 515
    Processing helix  chain 'C' and resid 518 through 531
    Processing helix  chain 'C' and resid 534 through 539
      removed outlier: 3.579A  pdb=" N   LEU C 538 " --> pdb=" O   PRO C 534 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 544 through 552
    Processing helix  chain 'C' and resid 558 through 564
    Processing helix  chain 'C' and resid 574 through 586
    Processing helix  chain 'C' and resid 588 through 601
    Processing helix  chain 'C' and resid 638 through 640
      No H-bonds generated for 'chain 'C' and resid 638 through 640'
    Processing helix  chain 'C' and resid 650 through 663
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25
    Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16
    Processing sheet with id=AA3, first strand: chain 'C' and resid 316 through 321
      removed outlier: 3.764A  pdb=" N   VAL C 321 " --> pdb=" O   ARG C 349 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 381 through 383
    Processing sheet with id=AA5, first strand: chain 'C' and resid 475 through 479
      removed outlier: 3.699A  pdb=" N   GLU C 482 " --> pdb=" O   ARG C 479 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 565 through 568

    228 hydrogen bonds defined for protein.
    626 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.97

  Time building geometry restraints manager: 1.59 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 820
        1.27 -     1.40: 1233
        1.40 -     1.54: 2853
        1.54 -     1.67: 53
        1.67 -     1.81: 24
  Bond restraints: 4983
  Sorted by residual:
  bond pdb=" C04 A1AIV B 101 "
       pdb=" C05 A1AIV B 101 "
    ideal  model  delta    sigma   weight residual
    1.453  1.525 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" N   MET A   1 "
       pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.96e+00
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.81e+00
  bond pdb=" C05 A1AIV B 101 "
       pdb=" N06 A1AIV B 101 "
    ideal  model  delta    sigma   weight residual
    1.151  1.132  0.019 2.00e-02 2.50e+03 9.21e-01
  bond pdb=" CG  LEU C 595 "
       pdb=" CD2 LEU C 595 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.11e-01
  ... (remaining 4978 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.77: 6352
        0.77 -     1.54: 331
        1.54 -     2.31: 29
        2.31 -     3.08: 9
        3.08 -     3.85: 26
  Bond angle restraints: 6747
  Sorted by residual:
  angle pdb=" N   LEU C 424 "
        pdb=" CA  LEU C 424 "
        pdb=" C   LEU C 424 "
      ideal   model   delta    sigma   weight residual
     109.79  107.61    2.18 1.56e+00 4.11e-01 1.96e+00
  angle pdb=" N   VAL C 515 "
        pdb=" CA  VAL C 515 "
        pdb=" C   VAL C 515 "
      ideal   model   delta    sigma   weight residual
     109.34  111.99   -2.65 2.08e+00 2.31e-01 1.63e+00
  angle pdb=" N   GLY B  75 "
        pdb=" CA  GLY B  75 "
        pdb=" C   GLY B  75 "
      ideal   model   delta    sigma   weight residual
     113.30  109.74    3.56 2.90e+00 1.19e-01 1.51e+00
  angle pdb=" C   SER A  19 "
        pdb=" CA  SER A  19 "
        pdb=" CB  SER A  19 "
      ideal   model   delta    sigma   weight residual
     110.65  108.56    2.09 1.95e+00 2.63e-01 1.15e+00
  angle pdb=" N   GLY A  82 "
        pdb=" CA  GLY A  82 "
        pdb=" C   GLY A  82 "
      ideal   model   delta    sigma   weight residual
     114.95  113.49    1.46 1.41e+00 5.03e-01 1.08e+00
  ... (remaining 6742 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.30: 2818
       14.30 -    28.59: 166
       28.59 -    42.89: 30
       42.89 -    57.19: 2
       57.19 -    71.48: 2
  Dihedral angle restraints: 3018
    sinusoidal: 1254
      harmonic: 1764
  Sorted by residual:
  dihedral pdb=" CA  VAL C 515 "
           pdb=" C   VAL C 515 "
           pdb=" N   THR C 516 "
           pdb=" CA  THR C 516 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.59  -16.41     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  ASP C 357 "
           pdb=" CB  ASP C 357 "
           pdb=" CG  ASP C 357 "
           pdb=" OD1 ASP C 357 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.35   51.35     1      2.00e+01 2.50e-03 9.01e+00
  dihedral pdb=" N   LEU C 509 "
           pdb=" CA  LEU C 509 "
           pdb=" CB  LEU C 509 "
           pdb=" CG  LEU C 509 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -103.44   43.44     3      1.50e+01 4.44e-03 7.81e+00
  ... (remaining 3015 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 450
       0.028 -    0.056: 192
       0.056 -    0.084: 51
       0.084 -    0.112: 30
       0.112 -    0.140: 14
  Chirality restraints: 737
  Sorted by residual:
  chirality pdb=" CA  ILE A  54 "
            pdb=" N   ILE A  54 "
            pdb=" C   ILE A  54 "
            pdb=" CB  ILE A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ILE C 533 "
            pdb=" N   ILE C 533 "
            pdb=" C   ILE C 533 "
            pdb=" CB  ILE C 533 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  ILE C 645 "
            pdb=" N   ILE C 645 "
            pdb=" C   ILE C 645 "
            pdb=" CB  ILE C 645 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 734 not shown)

  Planarity restraints: 873
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A  75 "    0.023 5.00e-02 4.00e+02   3.43e-02 1.88e+00
        pdb=" N   PRO A  76 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A  76 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A  76 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 430 "    0.019 5.00e-02 4.00e+02   2.94e-02 1.38e+00
        pdb=" N   PRO C 431 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C 431 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 431 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  94 "   -0.016 5.00e-02 4.00e+02   2.39e-02 9.18e-01
        pdb=" N   PRO A  95 "    0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 870 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.41: 6
        2.41 -     3.03: 2955
        3.03 -     3.65: 6690
        3.65 -     4.28: 10351
        4.28 -     4.90: 17782
  Nonbonded interactions: 37784
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C 639 "
            pdb=" C03 A1AIV B 101 "
     model   vdw
     1.782 3.800
  nonbonded pdb=" OG  SER C 397 "
            pdb=" OE1 GLN C 521 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OG  SER C 608 "
            pdb=" OD2 ASP C 612 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" OE2 GLU A   9 "
            pdb=" OH  TYR A  60 "
     model   vdw
     2.380 3.040
  nonbonded pdb=" ND2 ASN C 478 "
            pdb=" O   GLY C 481 "
     model   vdw
     2.392 3.120
  ... (remaining 37779 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=0.34 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.680
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     20.700
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.070
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
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      :  0.003   0.117   4985  Z= 0.213
  Angle     :  0.435   3.846   6747  Z= 0.217
  Chirality :  0.039   0.140    737
  Planarity :  0.003   0.034    873
  Dihedral  :  9.362  71.483   1878
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  3.87 %
    Favored  : 94.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.85 (0.37), residues: 594
  helix:  2.12 (0.34), residues: 252
  sheet:  1.04 (0.56), residues: 97
  loop :  0.47 (0.45), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 581 
 HIS   0.001   0.000   HIS C 420 
 PHE   0.009   0.001   PHE C 580 
 TYR   0.009   0.001   TYR C 367 
 ARG   0.002   0.000   ARG C 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13805 (  228)
  hydrogen bonds       : angle       5.73785 (  626)
  covalent geometry    : bond        0.00307 ( 4983)
  covalent geometry    : angle       0.43505 ( 6747)
  Misc. bond           : bond        0.08288 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7737 (pt0) cc_final: 0.7533 (tt0)
REVERT: A   66 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8160 (tttm)
REVERT: A   87 ASP cc_start: 0.8764 (p0) cc_final: 0.8335 (p0)
REVERT: A   91 ASP cc_start: 0.8054 (t0) cc_final: 0.7420 (t0)
REVERT: A  114 ASN cc_start: 0.7940 (t0) cc_final: 0.6212 (t0)
REVERT: A  130 ASP cc_start: 0.7058 (t0) cc_final: 0.6337 (t0)
REVERT: A  140 GLU cc_start: 0.8771 (mm-30) cc_final: 0.7906 (mm-30)
REVERT: B    1 MET cc_start: 0.1932 (ptt) cc_final: 0.1383 (ptt)
REVERT: C  554 ARG cc_start: 0.8647 (ttm110) cc_final: 0.8234 (ttm-80)
REVERT: C  640 PHE cc_start: 0.8417 (t80) cc_final: 0.8206 (t80)
  outliers start: 7
  outliers final: 2
  residues processed: 99
  average time/residue: 0.2630
  time to fit residues: 31.1695
Evaluate side-chains
  58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue  587 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0070
   chunk 15 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 17 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.134755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.084760 restraints weight = 13016.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 4.45
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3227
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3227 r_free = 0.3227    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3227 r_free = 0.3227    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3227
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4985  Z= 0.153
  Angle     :  0.540   6.566   6747  Z= 0.274
  Chirality :  0.041   0.133    737
  Planarity :  0.004   0.034    873
  Dihedral  :  4.719  47.745    664
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.21 %
    Favored  : 89.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.79 (0.37), residues: 594
  helix:  2.03 (0.34), residues: 254
  sheet:  1.11 (0.56), residues: 95
  loop :  0.43 (0.45), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 
 PHE   0.011   0.001   PHE C 522 
 TYR   0.011   0.001   TYR A 145 
 ARG   0.006   0.001   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03692 (  228)
  hydrogen bonds       : angle       4.70968 (  626)
  covalent geometry    : bond        0.00367 ( 4983)
  covalent geometry    : angle       0.53954 ( 6747)
  Misc. bond           : bond        0.00154 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8319 (tttm)
REVERT: A  140 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8042 (mm-30)
REVERT: C  554 ARG cc_start: 0.8628 (ttm110) cc_final: 0.8227 (ttm-80)
  outliers start: 7
  outliers final: 7
  residues processed: 68
  average time/residue: 0.2101
  time to fit residues: 17.8932
Evaluate side-chains
  54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  587 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0870
   chunk 21 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.6158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.133721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.084831 restraints weight = 10600.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 3.97
r_work: 0.3015 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4985  Z= 0.157
  Angle     :  0.525   7.213   6747  Z= 0.265
  Chirality :  0.041   0.134    737
  Planarity :  0.004   0.037    873
  Dihedral  :  4.760  49.582    664
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 10.13 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.82 (0.37), residues: 594
  helix:  2.07 (0.34), residues: 254
  sheet:  1.11 (0.57), residues: 95
  loop :  0.42 (0.45), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 
 PHE   0.012   0.001   PHE C 522 
 TYR   0.010   0.001   TYR A 145 
 ARG   0.005   0.000   ARG C 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03536 (  228)
  hydrogen bonds       : angle       4.61151 (  626)
  covalent geometry    : bond        0.00380 ( 4983)
  covalent geometry    : angle       0.52493 ( 6747)
  Misc. bond           : bond        0.00024 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8374 (tttm)
REVERT: A   81 ASN cc_start: 0.8718 (m110) cc_final: 0.8425 (m110)
REVERT: A  140 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8434 (mm-30)
REVERT: C  554 ARG cc_start: 0.8734 (ttm110) cc_final: 0.8367 (ttm-80)
  outliers start: 10
  outliers final: 9
  residues processed: 56
  average time/residue: 0.2305
  time to fit residues: 16.1494
Evaluate side-chains
  56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue  310 MET
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  587 TRP
Chi-restraints excluded: chain C residue  640 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:   20.0000
   chunk 35 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 51 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 27 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.133579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.082308 restraints weight = 16567.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 4.91
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4985  Z= 0.146
  Angle     :  0.510   6.873   6747  Z= 0.258
  Chirality :  0.040   0.134    737
  Planarity :  0.004   0.048    873
  Dihedral  :  4.770  50.121    664
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.68 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.89 (0.37), residues: 594
  helix:  2.18 (0.34), residues: 252
  sheet:  1.10 (0.56), residues: 95
  loop :  0.43 (0.45), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 
 PHE   0.011   0.001   PHE C 522 
 TYR   0.012   0.001   TYR A 145 
 ARG   0.006   0.001   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03361 (  228)
  hydrogen bonds       : angle       4.51236 (  626)
  covalent geometry    : bond        0.00355 ( 4983)
  covalent geometry    : angle       0.50966 ( 6747)
  Misc. bond           : bond        0.00034 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8311 (tttm)
REVERT: A   81 ASN cc_start: 0.8703 (m110) cc_final: 0.8472 (m110)
REVERT: A  140 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8061 (mm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 56
  average time/residue: 0.2179
  time to fit residues: 15.3614
Evaluate side-chains
  53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue  310 MET
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  587 TRP
Chi-restraints excluded: chain C residue  640 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 40 optimal weight:    0.4980
   chunk 20 optimal weight:   20.0000
   chunk 32 optimal weight:    0.6980
   chunk 15 optimal weight:   20.0000
   chunk 13 optimal weight:    0.2980
   chunk 10 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0050
   overall best weight:    0.3594

-------------------------------------------------------------------------------
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 = 0.3844 r_free = 0.3844 target = 0.134833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.084538 restraints weight = 21937.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 6.09
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3138
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4985  Z= 0.112
  Angle     :  0.487   6.924   6747  Z= 0.247
  Chirality :  0.040   0.132    737
  Planarity :  0.004   0.037    873
  Dihedral  :  4.711  50.193    664
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.87 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  2.00 (0.37), residues: 594
  helix:  2.24 (0.34), residues: 253
  sheet:  1.19 (0.57), residues: 95
  loop :  0.52 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 
 PHE   0.008   0.001   PHE C 522 
 TYR   0.008   0.001   TYR C 419 
 ARG   0.007   0.000   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03079 (  228)
  hydrogen bonds       : angle       4.42796 (  626)
  covalent geometry    : bond        0.00268 ( 4983)
  covalent geometry    : angle       0.48683 ( 6747)
  Misc. bond           : bond        0.00022 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8305 (tttm)
REVERT: A   92 GLN cc_start: 0.8711 (mp10) cc_final: 0.8316 (mp10)
REVERT: A  140 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8184 (mm-30)
REVERT: C  640 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7507 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 54
  average time/residue: 0.2628
  time to fit residues: 17.3893
Evaluate side-chains
  58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue  310 MET
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  587 TRP
Chi-restraints excluded: chain C residue  640 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 51 optimal weight:    0.6980
   chunk 14 optimal weight:   10.0000
   chunk 21 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3834 r_free = 0.3834 target = 0.134133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.085238 restraints weight = 10618.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 3.98
r_work: 0.2931 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4985  Z= 0.136
  Angle     :  0.500   7.325   6747  Z= 0.253
  Chirality :  0.040   0.134    737
  Planarity :  0.004   0.037    873
  Dihedral  :  4.741  50.950    664
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.42 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  2.01 (0.37), residues: 594
  helix:  2.26 (0.34), residues: 253
  sheet:  1.16 (0.57), residues: 95
  loop :  0.52 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 
 PHE   0.011   0.001   PHE C 522 
 TYR   0.008   0.001   TYR C 419 
 ARG   0.008   0.001   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03165 (  228)
  hydrogen bonds       : angle       4.44085 (  626)
  covalent geometry    : bond        0.00330 ( 4983)
  covalent geometry    : angle       0.49961 ( 6747)
  Misc. bond           : bond        0.00003 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8324 (tttm)
REVERT: A   92 GLN cc_start: 0.8953 (mp10) cc_final: 0.8316 (mp10)
REVERT: A  140 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8292 (mm-30)
REVERT: A  143 ARG cc_start: 0.8775 (tmm-80) cc_final: 0.8069 (tmm-80)
REVERT: C  640 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7863 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 54
  average time/residue: 0.1941
  time to fit residues: 13.5815
Evaluate side-chains
  54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue  310 MET
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  587 TRP
Chi-restraints excluded: chain C residue  640 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 55 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0020
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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 = 0.3834 r_free = 0.3834 target = 0.134117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.083793 restraints weight = 21955.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 6.07
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4985  Z= 0.135
  Angle     :  0.497   7.486   6747  Z= 0.252
  Chirality :  0.040   0.134    737
  Planarity :  0.004   0.037    873
  Dihedral  :  4.738  50.811    664
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.42 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  2.00 (0.37), residues: 594
  helix:  2.25 (0.34), residues: 253
  sheet:  1.15 (0.57), residues: 95
  loop :  0.51 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 
 PHE   0.010   0.001   PHE C 522 
 TYR   0.008   0.001   TYR C 419 
 ARG   0.005   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03150 (  228)
  hydrogen bonds       : angle       4.43370 (  626)
  covalent geometry    : bond        0.00328 ( 4983)
  covalent geometry    : angle       0.49673 ( 6747)
  Misc. bond           : bond        0.00032 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8312 (tttm)
REVERT: A   92 GLN cc_start: 0.8727 (mp10) cc_final: 0.8054 (mp10)
REVERT: A  140 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8189 (mm-30)
REVERT: A  143 ARG cc_start: 0.8660 (tmm-80) cc_final: 0.7971 (tmm-80)
REVERT: C  640 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7582 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 53
  average time/residue: 0.2158
  time to fit residues: 14.4243
Evaluate side-chains
  54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue  310 MET
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  587 TRP
Chi-restraints excluded: chain C residue  640 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 40 optimal weight:    0.3980
   chunk 56 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0980
   chunk 24 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 49 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 = 0.3835 r_free = 0.3835 target = 0.134230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.084155 restraints weight = 13072.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 4.44
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3222
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3222 r_free = 0.3222    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3222 r_free = 0.3222    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3222
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4985  Z= 0.128
  Angle     :  0.500   8.019   6747  Z= 0.254
  Chirality :  0.040   0.133    737
  Planarity :  0.003   0.037    873
  Dihedral  :  4.732  50.851    664
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.42 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  2.00 (0.37), residues: 594
  helix:  2.24 (0.34), residues: 253
  sheet:  1.19 (0.57), residues: 95
  loop :  0.52 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 
 PHE   0.010   0.001   PHE C 522 
 TYR   0.008   0.001   TYR C 419 
 ARG   0.004   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03164 (  228)
  hydrogen bonds       : angle       4.46360 (  626)
  covalent geometry    : bond        0.00311 ( 4983)
  covalent geometry    : angle       0.49981 ( 6747)
  Misc. bond           : bond        0.00009 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8330 (tttm)
REVERT: A   92 GLN cc_start: 0.8735 (mp10) cc_final: 0.8185 (mp10)
REVERT: A  140 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8095 (mm-30)
REVERT: A  143 ARG cc_start: 0.8612 (tmm-80) cc_final: 0.8027 (tmm-80)
REVERT: C  640 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7570 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 51
  average time/residue: 0.2223
  time to fit residues: 14.9037
Evaluate side-chains
  53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue  310 MET
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  587 TRP
Chi-restraints excluded: chain C residue  640 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 18 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0070
   chunk 13 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5998

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.131277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.083562 restraints weight = 12813.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 4.51
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3139
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3139
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4985  Z= 0.154
  Angle     :  0.517   8.255   6747  Z= 0.261
  Chirality :  0.041   0.133    737
  Planarity :  0.004   0.038    873
  Dihedral  :  4.763  50.885    664
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.60 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.96 (0.37), residues: 594
  helix:  2.21 (0.34), residues: 253
  sheet:  1.15 (0.57), residues: 95
  loop :  0.50 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 
 PHE   0.012   0.001   PHE C 522 
 TYR   0.009   0.001   TYR C 419 
 ARG   0.005   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03278 (  228)
  hydrogen bonds       : angle       4.50623 (  626)
  covalent geometry    : bond        0.00376 ( 4983)
  covalent geometry    : angle       0.51724 ( 6747)
  Misc. bond           : bond        0.00032 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8228 (tttm)
REVERT: A   92 GLN cc_start: 0.8764 (mp10) cc_final: 0.8200 (mp10)
REVERT: A  140 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8125 (mm-30)
REVERT: A  143 ARG cc_start: 0.8633 (tmm-80) cc_final: 0.7996 (tmm-80)
REVERT: C  640 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7600 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 49
  average time/residue: 0.3356
  time to fit residues: 20.7553
Evaluate side-chains
  53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue  310 MET
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  587 TRP
Chi-restraints excluded: chain C residue  640 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 14 optimal weight:    0.3980
   chunk 57 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0770
   chunk 13 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.131449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.084594 restraints weight = 10908.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 4.17
r_work: 0.2940 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4985  Z= 0.144
  Angle     :  0.514   8.702   6747  Z= 0.260
  Chirality :  0.040   0.134    737
  Planarity :  0.004   0.037    873
  Dihedral  :  4.773  51.234    664
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.60 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.97 (0.37), residues: 594
  helix:  2.20 (0.34), residues: 253
  sheet:  1.16 (0.57), residues: 95
  loop :  0.51 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 
 PHE   0.011   0.001   PHE C 522 
 TYR   0.008   0.001   TYR C 419 
 ARG   0.004   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03247 (  228)
  hydrogen bonds       : angle       4.48674 (  626)
  covalent geometry    : bond        0.00353 ( 4983)
  covalent geometry    : angle       0.51440 ( 6747)
  Misc. bond           : bond        0.00008 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 1.401 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8263 (tttm)
REVERT: A   92 GLN cc_start: 0.8945 (mp10) cc_final: 0.8368 (mp10)
REVERT: A  140 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8384 (mm-30)
REVERT: A  143 ARG cc_start: 0.8760 (tmm-80) cc_final: 0.8112 (tmm-80)
REVERT: C  640 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7950 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 49
  average time/residue: 0.3279
  time to fit residues: 21.4285
Evaluate side-chains
  54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue  310 MET
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  587 TRP
Chi-restraints excluded: chain C residue  640 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 53 optimal weight:    0.4980
   chunk 41 optimal weight:    0.0050
   chunk 29 optimal weight:    0.2980
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.3994

-------------------------------------------------------------------------------
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 = 0.3795 r_free = 0.3795 target = 0.132019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.080432 restraints weight = 18159.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 5.24
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4985  Z= 0.116
  Angle     :  0.499   9.371   6747  Z= 0.252
  Chirality :  0.040   0.132    737
  Planarity :  0.004   0.037    873
  Dihedral  :  4.715  51.336    664
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.42 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  2.06 (0.37), residues: 594
  helix:  2.28 (0.34), residues: 253
  sheet:  1.21 (0.57), residues: 95
  loop :  0.56 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  93 
 HIS   0.002   0.000   HIS C 420 
 PHE   0.008   0.001   PHE C 522 
 TYR   0.008   0.001   TYR C 419 
 ARG   0.005   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03060 (  228)
  hydrogen bonds       : angle       4.41586 (  626)
  covalent geometry    : bond        0.00283 ( 4983)
  covalent geometry    : angle       0.49908 ( 6747)
  Misc. bond           : bond        0.00012 (    2)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 3399.76 seconds
wall clock time: 61 minutes 0.46 seconds (3660.46 seconds total)