Starting phenix.real_space_refine
on Fri Aug 22 15:23:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5b_44206/08_2025/9b5b_44206.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5b_44206/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5b_44206/08_2025/9b5b_44206.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5b_44206/08_2025/9b5b_44206.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5b_44206/08_2025/9b5b_44206.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5b_44206/08_2025/9b5b_44206.map"
  }
  resolution = 3.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.91, per 1000 atoms: 0.39
  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: 0.54
  Conformation dependent library (CDL) restraints added in 189.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.27
  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: 0.68

  Time building geometry restraints manager: 0.68 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:             2.200
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.110
  Find NCS groups from input model:        0.020
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.530
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG C 412 
 TYR   0.009   0.001   TYR C 367 
 PHE   0.009   0.001   PHE C 580 
 TRP   0.006   0.001   TRP C 581 
 HIS   0.001   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4983)
  covalent geometry    : angle       0.43505 ( 6747)
  hydrogen bonds       : bond        0.13805 (  228)
  hydrogen bonds       : angle       5.73785 (  626)
  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  : 0.180 
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: 0.0910
  time to fit residues: 10.7782
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  : 0.212 
-------------------------------------------------------------------------------
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 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0070
   chunk 48 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0570
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.3716

-------------------------------------------------------------------------------
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 = 0.3859 r_free = 0.3859 target = 0.135802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.084235 restraints weight = 17929.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 5.20
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4985  Z= 0.122
  Angle     :  0.513   6.388   6747  Z= 0.261
  Chirality :  0.040   0.131    737
  Planarity :  0.004   0.034    873
  Dihedral  :  4.592  47.933    664
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.21 %
    Favored  : 89.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.37), residues: 594
  helix:  2.11 (0.34), residues: 254
  sheet:  1.18 (0.56), residues: 95
  loop :  0.47 (0.45), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 139 
 TYR   0.011   0.001   TYR A 145 
 PHE   0.009   0.001   PHE C 522 
 TRP   0.006   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4983)
  covalent geometry    : angle       0.51275 ( 6747)
  hydrogen bonds       : bond        0.03511 (  228)
  hydrogen bonds       : angle       4.65402 (  626)
  Misc. bond           : bond        0.00036 (    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
  69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8321 (tttm)
REVERT: A  140 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8096 (mm-30)
REVERT: C  554 ARG cc_start: 0.8673 (ttm110) cc_final: 0.8215 (ttm-80)
  outliers start: 6
  outliers final: 6
  residues processed: 67
  average time/residue: 0.0929
  time to fit residues: 7.7225
Evaluate side-chains
  52 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
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 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 53 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   chunk 50 optimal weight:    0.1980
   chunk 46 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0870
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.134947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.083837 restraints weight = 16524.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 4.91
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4985  Z= 0.121
  Angle     :  0.503   7.234   6747  Z= 0.256
  Chirality :  0.040   0.164    737
  Planarity :  0.004   0.034    873
  Dihedral  :  4.607  49.923    664
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.58 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.37), residues: 594
  helix:  2.17 (0.34), residues: 255
  sheet:  1.24 (0.57), residues: 95
  loop :  0.50 (0.45), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  72 
 TYR   0.008   0.001   TYR A 145 
 PHE   0.010   0.001   PHE C 522 
 TRP   0.006   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4983)
  covalent geometry    : angle       0.50287 ( 6747)
  hydrogen bonds       : bond        0.03239 (  228)
  hydrogen bonds       : angle       4.50994 (  626)
  Misc. bond           : bond        0.00030 (    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
  58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8335 (tttm)
REVERT: A   81 ASN cc_start: 0.8672 (m110) cc_final: 0.8395 (m110)
REVERT: A  140 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8138 (mm-30)
REVERT: C  554 ARG cc_start: 0.8694 (ttm110) cc_final: 0.8263 (ttm-80)
  outliers start: 9
  outliers final: 9
  residues processed: 55
  average time/residue: 0.0947
  time to fit residues: 6.4256
Evaluate side-chains
  55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
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 44 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 29 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0060
   chunk 45 optimal weight:    0.0770
   chunk 39 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 52 optimal weight:    0.3980
   overall best weight:    0.3154

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.135328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.083921 restraints weight = 17889.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 5.05
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    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 = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.1904

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= 0.105
  Angle     :  0.490   7.213   6747  Z= 0.247
  Chirality :  0.040   0.164    737
  Planarity :  0.004   0.051    873
  Dihedral  :  4.590  50.296    664
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.94 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.37), residues: 594
  helix:  2.28 (0.34), residues: 255
  sheet:  1.26 (0.57), residues: 95
  loop :  0.51 (0.45), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  72 
 TYR   0.009   0.001   TYR A 145 
 PHE   0.009   0.001   PHE C 522 
 TRP   0.005   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 4983)
  covalent geometry    : angle       0.48999 ( 6747)
  hydrogen bonds       : bond        0.03016 (  228)
  hydrogen bonds       : angle       4.42568 (  626)
  Misc. bond           : bond        0.00018 (    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
  58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8319 (tttm)
REVERT: A   81 ASN cc_start: 0.8692 (m110) cc_final: 0.8477 (m110)
REVERT: A  140 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8079 (mm-30)
  outliers start: 11
  outliers final: 10
  residues processed: 54
  average time/residue: 0.1092
  time to fit residues: 7.1420
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  : 0.193 
-------------------------------------------------------------------------------
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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 15 optimal weight:   20.0000
   chunk 10 optimal weight:    0.2980
   chunk 9 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9980
   chunk 47 optimal weight:    0.3980
   chunk 52 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.6182

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.134263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.084321 restraints weight = 12689.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 4.34
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1969

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= 0.153
  Angle     :  0.506   6.986   6747  Z= 0.255
  Chirality :  0.041   0.150    737
  Planarity :  0.004   0.038    873
  Dihedral  :  4.646  50.078    664
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.50 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.37), residues: 594
  helix:  2.23 (0.34), residues: 255
  sheet:  1.18 (0.57), residues: 95
  loop :  0.46 (0.45), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 349 
 TYR   0.009   0.001   TYR A 145 
 PHE   0.013   0.001   PHE C 522 
 TRP   0.007   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 4983)
  covalent geometry    : angle       0.50551 ( 6747)
  hydrogen bonds       : bond        0.03213 (  228)
  hydrogen bonds       : angle       4.45624 (  626)
  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
  58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8044 (mm-30)
  outliers start: 11
  outliers final: 10
  residues processed: 54
  average time/residue: 0.0836
  time to fit residues: 5.7970
Evaluate side-chains
  55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0770
   chunk 5 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.134490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.083207 restraints weight = 16640.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 4.93
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3197
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4985  Z= 0.132
  Angle     :  0.496   7.336   6747  Z= 0.251
  Chirality :  0.040   0.150    737
  Planarity :  0.004   0.035    873
  Dihedral  :  4.664  50.403    664
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.05 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.37), residues: 594
  helix:  2.29 (0.34), residues: 253
  sheet:  1.25 (0.57), residues: 95
  loop :  0.51 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 349 
 TYR   0.013   0.001   TYR A 145 
 PHE   0.010   0.001   PHE C 522 
 TRP   0.006   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4983)
  covalent geometry    : angle       0.49560 ( 6747)
  hydrogen bonds       : bond        0.03122 (  228)
  hydrogen bonds       : angle       4.41300 (  626)
  Misc. bond           : bond        0.00022 (    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
  57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 ASN cc_start: 0.8885 (p0) cc_final: 0.8575 (p0)
REVERT: A  140 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8029 (mm-30)
REVERT: A  143 ARG cc_start: 0.8721 (tmm-80) cc_final: 0.8026 (tmm-80)
REVERT: C  640 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7500 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 53
  average time/residue: 0.0885
  time to fit residues: 5.8631
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  : 0.164 
-------------------------------------------------------------------------------
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 7 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0970
   chunk 6 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.133613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.082471 restraints weight = 16634.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 4.88
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2119

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= 0.155
  Angle     :  0.518   7.604   6747  Z= 0.263
  Chirality :  0.041   0.148    737
  Planarity :  0.004   0.038    873
  Dihedral  :  4.752  51.207    664
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.23 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.37), residues: 594
  helix:  2.20 (0.34), residues: 253
  sheet:  1.29 (0.58), residues: 95
  loop :  0.48 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 139 
 TYR   0.008   0.001   TYR C 419 
 PHE   0.012   0.001   PHE C 522 
 TRP   0.007   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 4983)
  covalent geometry    : angle       0.51784 ( 6747)
  hydrogen bonds       : bond        0.03281 (  228)
  hydrogen bonds       : angle       4.50585 (  626)
  Misc. bond           : bond        0.00036 (    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
  57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 ASN cc_start: 0.8908 (p0) cc_final: 0.8651 (p0)
REVERT: A  140 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8112 (mm-30)
REVERT: A  143 ARG cc_start: 0.8637 (tmm-80) cc_final: 0.8028 (tmm-80)
REVERT: C  640 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7539 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 53
  average time/residue: 0.0943
  time to fit residues: 6.1816
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  : 0.196 
-------------------------------------------------------------------------------
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 23 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0050
   chunk 26 optimal weight:    0.5980
   chunk 54 optimal weight:    0.3980
   chunk 33 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.4394

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.134385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.087591 restraints weight = 8115.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 3.41
r_work: 0.3056 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4985  Z= 0.125
  Angle     :  0.509   8.068   6747  Z= 0.259
  Chirality :  0.040   0.149    737
  Planarity :  0.004   0.037    873
  Dihedral  :  4.722  51.480    664
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.87 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.38), residues: 594
  helix:  2.24 (0.34), residues: 253
  sheet:  1.36 (0.58), residues: 95
  loop :  0.52 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 139 
 TYR   0.008   0.001   TYR C 419 
 PHE   0.009   0.001   PHE C 522 
 TRP   0.006   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 4983)
  covalent geometry    : angle       0.50938 ( 6747)
  hydrogen bonds       : bond        0.03138 (  228)
  hydrogen bonds       : angle       4.43738 (  626)
  Misc. bond           : bond        0.00035 (    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
  62 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.8434 (mtp85) cc_final: 0.7997 (mtp85)
REVERT: A   91 ASP cc_start: 0.8456 (t0) cc_final: 0.8210 (t0)
REVERT: A  140 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8288 (mm-30)
REVERT: A  143 ARG cc_start: 0.8715 (tmm-80) cc_final: 0.8074 (tmm-80)
REVERT: C  543 GLU cc_start: 0.8270 (pm20) cc_final: 0.8057 (pt0)
REVERT: C  640 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7832 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 57
  average time/residue: 0.0886
  time to fit residues: 6.2096
Evaluate side-chains
  56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   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 = 0.3821 r_free = 0.3821 target = 0.133038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.083059 restraints weight = 13090.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 4.39
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3198
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3198
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4985  Z= 0.167
  Angle     :  0.536   8.473   6747  Z= 0.271
  Chirality :  0.041   0.146    737
  Planarity :  0.004   0.039    873
  Dihedral  :  4.797  51.190    664
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.05 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.96 (0.37), residues: 594
  helix:  2.17 (0.34), residues: 253
  sheet:  1.32 (0.58), residues: 95
  loop :  0.47 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 139 
 TYR   0.009   0.001   TYR C 419 
 PHE   0.014   0.001   PHE C 522 
 TRP   0.007   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 4983)
  covalent geometry    : angle       0.53556 ( 6747)
  hydrogen bonds       : bond        0.03359 (  228)
  hydrogen bonds       : angle       4.49210 (  626)
  Misc. bond           : bond        0.00050 (    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
  58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7752 (mtp85)
REVERT: A   80 SER cc_start: 0.9243 (t) cc_final: 0.8784 (p)
REVERT: A   91 ASP cc_start: 0.8090 (t0) cc_final: 0.7886 (t0)
REVERT: A  140 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7988 (mm-30)
REVERT: A  143 ARG cc_start: 0.8610 (tmm-80) cc_final: 0.7949 (tmm-80)
REVERT: C  640 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7547 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 54
  average time/residue: 0.0753
  time to fit residues: 5.0442
Evaluate side-chains
  57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
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 36 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 7 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0970
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.133734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.083710 restraints weight = 13475.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 4.46
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4985  Z= 0.135
  Angle     :  0.526   9.071   6747  Z= 0.267
  Chirality :  0.040   0.148    737
  Planarity :  0.004   0.038    873
  Dihedral  :  4.788  51.751    664
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.42 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.38), residues: 594
  helix:  2.23 (0.34), residues: 253
  sheet:  1.34 (0.58), residues: 95
  loop :  0.53 (0.46), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 139 
 TYR   0.008   0.001   TYR C 419 
 PHE   0.011   0.001   PHE C 522 
 TRP   0.007   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 4983)
  covalent geometry    : angle       0.52643 ( 6747)
  hydrogen bonds       : bond        0.03223 (  228)
  hydrogen bonds       : angle       4.44773 (  626)
  Misc. bond           : bond        0.00040 (    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
  56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7595 (mtp85)
REVERT: A  140 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7971 (mm-30)
REVERT: A  143 ARG cc_start: 0.8624 (tmm-80) cc_final: 0.7958 (tmm-80)
REVERT: C  640 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7582 (m-80)
  outliers start: 10
  outliers final: 9
  residues processed: 52
  average time/residue: 0.0867
  time to fit residues: 5.5645
Evaluate side-chains
  55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 28 optimal weight:    0.1980
   chunk 51 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0270
   chunk 26 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0970
   chunk 54 optimal weight:    0.6980
   chunk 4 optimal weight:    0.1980
   overall best weight:    0.2236

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.135239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.086275 restraints weight = 11124.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 4.09
r_work: 0.3019 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   4985  Z= 0.101
  Angle     :  0.511  10.027   6747  Z= 0.259
  Chirality :  0.039   0.152    737
  Planarity :  0.004   0.037    873
  Dihedral  :  4.728  51.754    664
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.38), residues: 594
  helix:  2.31 (0.34), residues: 253
  sheet:  1.44 (0.58), residues: 95
  loop :  0.59 (0.46), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  74 
 TYR   0.006   0.001   TYR C 419 
 PHE   0.007   0.001   PHE C 407 
 TRP   0.008   0.001   TRP A  93 
 HIS   0.001   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 4983)
  covalent geometry    : angle       0.51069 ( 6747)
  hydrogen bonds       : bond        0.02962 (  228)
  hydrogen bonds       : angle       4.37029 (  626)
  Misc. bond           : bond        0.00013 (    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: 1266.84 seconds
wall clock time: 22 minutes 8.67 seconds (1328.67 seconds total)