Starting phenix.real_space_refine
on Tue Jan 14 01:29:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5a_44205/01_2025/9b5a_44205.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5a_44205/01_2025/9b5a_44205.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5a_44205/01_2025/9b5a_44205.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5a_44205/01_2025/9b5a_44205.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5a_44205/01_2025/9b5a_44205.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5a_44205/01_2025/9b5a_44205.cif"
  }
  resolution = 3.65
  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=   0.038
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

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 5.09, per 1000 atoms: 1.04
  Number of scatterers: 4871
  At special positions: 0
  Unit cell: (74.48, 82.992, 97.888, 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: 1.39
  Conformation dependent library (CDL) restraints added in 971.0 milliseconds
  

  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:
      30 helices and 6 sheets defined
      49.7% alpha, 10.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 16
      removed outlier: 3.834A  pdb=" N   ASP A  16 " --> pdb=" O   ASP A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 112
      removed outlier: 3.786A  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 307
    Processing helix  chain 'C' and resid 308 through 311
      removed outlier: 3.835A  pdb=" N   ALA C 311 " --> pdb=" O   PRO C 308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 308 through 311'
    Processing helix  chain 'C' and resid 326 through 335
      removed outlier: 3.577A  pdb=" N   SER C 335 " --> pdb=" O   TYR C 331 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 343
      removed outlier: 3.520A  pdb=" N   LYS C 343 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
    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
      removed outlier: 3.951A  pdb=" N   SER C 398 " --> pdb=" O   PRO C 395 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN C 400 " --> pdb=" O   SER C 397 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 420
      removed outlier: 4.070A  pdb=" N   TYR C 406 " --> pdb=" O   ASP C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 437
      removed outlier: 3.539A  pdb=" N   TYR C 433 " --> pdb=" O   VAL C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 444
      No H-bonds generated for 'chain 'C' and resid 442 through 444'
    Processing helix  chain 'C' and resid 445 through 450
      removed outlier: 4.007A  pdb=" N   VAL C 449 " --> pdb=" O   ASP C 445 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 450 through 463
    Processing helix  chain 'C' and resid 491 through 495
      removed outlier: 3.784A  pdb=" N   ASN C 494 " --> pdb=" O   ASN C 491 " (cutoff:3.500A)
      removed outlier: 3.713A  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 516 through 518
      No H-bonds generated for 'chain 'C' and resid 516 through 518'
    Processing helix  chain 'C' and resid 519 through 531
    Processing helix  chain 'C' and resid 534 through 539
    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
      removed outlier: 3.592A  pdb=" N   ILE C 578 " --> pdb=" O   ASP C 574 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 588 through 601
    Processing helix  chain 'C' and resid 608 through 613
      removed outlier: 3.917A  pdb=" N   LYS C 611 " --> pdb=" O   SER C 608 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP C 612 " --> pdb=" O   GLY C 609 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   MET C 613 " --> pdb=" O   PHE C 610 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 608 through 613'
    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 662
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 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: 3.533A  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: 3.773A  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
      removed outlier: 6.536A  pdb=" N   ASP C 566 " --> pdb=" O   ILE C 624 " (cutoff:3.500A)

    215 hydrogen bonds defined for protein.
    608 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: 1.28

  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 -     1.41: 1239
        1.41 -     1.54: 2895
        1.54 -     1.68: 5
        1.68 -     1.82: 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 1.31e+01
  bond pdb=" N   MET A   1 "
       pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.85e+00
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.69e+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 9.10e-01
  bond pdb=" CG  LEU C 595 "
       pdb=" CD2 LEU C 595 "
    ideal  model  delta    sigma   weight residual
    1.521  1.494  0.027 3.30e-02 9.18e+02 6.69e-01
  ... (remaining 4978 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.83: 6316
        0.83 -     1.65: 354
        1.65 -     2.48: 39
        2.48 -     3.30: 21
        3.30 -     4.13: 17
  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
     110.41  108.27    2.14 1.23e+00 6.61e-01 3.03e+00
  angle pdb=" C   LEU C 424 "
        pdb=" N   ASP C 425 "
        pdb=" CA  ASP C 425 "
      ideal   model   delta    sigma   weight residual
     122.62  120.33    2.29 1.63e+00 3.76e-01 1.97e+00
  angle pdb=" CA  TRP C 581 "
        pdb=" CB  TRP C 581 "
        pdb=" CG  TRP C 581 "
      ideal   model   delta    sigma   weight residual
     113.60  110.94    2.66 1.90e+00 2.77e-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  111.85   -2.51 2.08e+00 2.31e-01 1.45e+00
  angle pdb=" N   TYR C 423 "
        pdb=" CA  TYR C 423 "
        pdb=" C   TYR C 423 "
      ideal   model   delta    sigma   weight residual
     108.52  110.46   -1.94 1.63e+00 3.76e-01 1.42e+00
  ... (remaining 6742 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.48: 2647
       11.48 -    22.97: 278
       22.97 -    34.45: 73
       34.45 -    45.94: 17
       45.94 -    57.42: 3
  Dihedral angle restraints: 3018
    sinusoidal: 1254
      harmonic: 1764
  Sorted by residual:
  dihedral pdb=" CA  TYR C 423 "
           pdb=" C   TYR C 423 "
           pdb=" N   LEU C 424 "
           pdb=" CA  LEU C 424 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.93   23.07     0      5.00e+00 4.00e-02 2.13e+01
  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 -164.52  -15.48     0      5.00e+00 4.00e-02 9.58e+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 -110.67   50.67     3      1.50e+01 4.44e-03 8.93e+00
  ... (remaining 3015 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 443
       0.027 -    0.054: 197
       0.054 -    0.081: 49
       0.081 -    0.107: 31
       0.107 -    0.134: 17
  Chirality restraints: 737
  Sorted by residual:
  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 4.51e-01
  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    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  ILE B  44 "
            pdb=" N   ILE B  44 "
            pdb=" C   ILE B  44 "
            pdb=" CB  ILE B  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 734 not shown)

  Planarity restraints: 873
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A  75 "    0.025 5.00e-02 4.00e+02   3.83e-02 2.35e+00
        pdb=" N   PRO A  76 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A  76 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  76 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  94 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.36e+00
        pdb=" N   PRO A  95 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 430 "    0.018 5.00e-02 4.00e+02   2.79e-02 1.24e+00
        pdb=" N   PRO C 431 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO C 431 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C 431 "    0.016 5.00e-02 4.00e+02
  ... (remaining 870 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.40: 12
        2.40 -     3.03: 2981
        3.03 -     3.65: 6872
        3.65 -     4.28: 10171
        4.28 -     4.90: 17504
  Nonbonded interactions: 37540
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A  85 "
            pdb=" C03 A1AIV B 101 "
     model   vdw
     1.776 3.800
  nonbonded pdb=" OG  SER C 397 "
            pdb=" OE1 GLN C 521 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" N   ASP C 387 "
            pdb=" OD1 ASP C 387 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" O   VAL C 426 "
            pdb=" ND2 ASN C 551 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" OD1 ASP C 487 "
            pdb=" NH2 ARG C 493 "
     model   vdw
     2.344 3.120
  ... (remaining 37535 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=0.40 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.950
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     16.890
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
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   0.072   4983  Z= 0.225
  Angle     :  0.471   4.126   6747  Z= 0.242
  Chirality :  0.039   0.134    737
  Planarity :  0.003   0.038    873
  Dihedral  : 10.281  57.421   1878
  Min Nonbonded Distance : 1.776

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  5.34 %
    Favored  : 93.00 %
  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:  1.20 (0.36), residues: 594
  helix:  1.98 (0.34), residues: 254
  sheet:  0.84 (0.60), residues: 84
  loop : -0.40 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 581 
 HIS   0.005   0.001   HIS C 512 
 PHE   0.010   0.001   PHE C 407 
 TYR   0.011   0.001   TYR A  60 
 ARG   0.003   0.000   ARG C 412 

*********************** 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
  99 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.8913 (tpp80) cc_final: 0.8711 (mmm-85)
REVERT: A  135 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8075 (mt-10)
REVERT: C  386 ASP cc_start: 0.8388 (m-30) cc_final: 0.8134 (m-30)
REVERT: C  451 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7630 (mp0)
REVERT: C  570 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.5058 (m-80)
  outliers start: 9
  outliers final: 3
  residues processed: 96
  average time/residue: 0.2777
  time to fit residues: 31.5482
Evaluate side-chains
  55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  487 ASP
Chi-restraints excluded: chain C residue  570 TYR
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:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0470
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.6678

-------------------------------------------------------------------------------
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 = 0.116610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.085069 restraints weight = 19367.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.088022 restraints weight = 11781.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.090151 restraints weight = 8337.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3393
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4983  Z= 0.231
  Angle     :  0.544   6.047   6747  Z= 0.283
  Chirality :  0.040   0.134    737
  Planarity :  0.004   0.039    873
  Dihedral  :  5.689  72.724    667
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 11.42 %
    Favored  : 87.66 %
  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:  1.19 (0.36), residues: 594
  helix:  1.94 (0.34), residues: 262
  sheet:  0.83 (0.58), residues: 89
  loop : -0.48 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 581 
 HIS   0.003   0.001   HIS A  75 
 PHE   0.010   0.001   PHE C 622 
 TYR   0.017   0.001   TYR C 454 
 ARG   0.006   0.001   ARG A 139 

*********************** 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
  57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.8968 (tpp80) cc_final: 0.8570 (mmm-85)
REVERT: B    1 MET cc_start: 0.4608 (ptt) cc_final: 0.3472 (ppp)
REVERT: B   21 ASP cc_start: 0.7421 (m-30) cc_final: 0.7210 (m-30)
REVERT: B   61 ILE cc_start: -0.0092 (mt) cc_final: -0.0499 (mt)
REVERT: B   74 ARG cc_start: 0.7302 (tpp80) cc_final: 0.6792 (mpt180)
REVERT: C  343 LYS cc_start: 0.8588 (mttt) cc_final: 0.8182 (mtpp)
REVERT: C  570 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.5464 (m-80)
  outliers start: 5
  outliers final: 4
  residues processed: 57
  average time/residue: 0.2479
  time to fit residues: 17.4555
Evaluate side-chains
  50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain C residue  570 TYR
Chi-restraints excluded: chain C residue  571 THR
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:    0.0770
   chunk 38 optimal weight:    0.2980
   chunk 0 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 5 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.4138

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.119452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.088907 restraints weight = 15227.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.091867 restraints weight = 9410.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.093971 restraints weight = 6738.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3458
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3458 r_free = 0.3458    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3458 r_free = 0.3458    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3458
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4983  Z= 0.170
  Angle     :  0.488   6.599   6747  Z= 0.254
  Chirality :  0.039   0.135    737
  Planarity :  0.004   0.034    873
  Dihedral  :  5.711  77.962    664
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 10.31 %
    Favored  : 88.21 %
  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:  1.21 (0.36), residues: 594
  helix:  1.90 (0.34), residues: 262
  sheet:  0.87 (0.58), residues: 89
  loop : -0.41 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 581 
 HIS   0.002   0.000   HIS A  75 
 PHE   0.016   0.001   PHE C 640 
 TYR   0.011   0.001   TYR C 454 
 ARG   0.004   0.000   ARG A 139 

*********************** 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
  56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8140 (tmtt)
REVERT: A  131 ARG cc_start: 0.8829 (tpp80) cc_final: 0.8540 (mmm-85)
REVERT: B    1 MET cc_start: 0.4588 (ptt) cc_final: 0.3816 (ppp)
REVERT: B   21 ASP cc_start: 0.7110 (m-30) cc_final: 0.6829 (m-30)
REVERT: B   61 ILE cc_start: -0.0101 (mt) cc_final: -0.0440 (mt)
REVERT: B   74 ARG cc_start: 0.7232 (tpp80) cc_final: 0.6835 (mpt180)
REVERT: C  343 LYS cc_start: 0.8484 (mttt) cc_final: 0.8265 (mtpp)
REVERT: C  570 TYR cc_start: 0.6021 (OUTLIER) cc_final: 0.5370 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 55
  average time/residue: 0.2338
  time to fit residues: 16.0378
Evaluate side-chains
  51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  570 TYR
Chi-restraints excluded: chain C residue  571 THR
Chi-restraints excluded: chain C residue  587 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 35 optimal weight:    0.1980
   chunk 52 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0970
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.3862 r_free = 0.3862 target = 0.118861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.089285 restraints weight = 23726.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.093293 restraints weight = 13152.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.095732 restraints weight = 8164.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3478
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3478
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4983  Z= 0.186
  Angle     :  0.498   7.369   6747  Z= 0.255
  Chirality :  0.040   0.145    737
  Planarity :  0.004   0.042    873
  Dihedral  :  5.746  79.099    664
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.42 %
    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:  1.20 (0.37), residues: 594
  helix:  1.87 (0.34), residues: 262
  sheet:  0.95 (0.58), residues: 89
  loop : -0.43 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 581 
 HIS   0.002   0.001   HIS A  75 
 PHE   0.009   0.001   PHE C 640 
 TYR   0.018   0.001   TYR C 454 
 ARG   0.005   0.000   ARG A 133 

*********************** 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
  56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8258 (tmtt)
REVERT: A  131 ARG cc_start: 0.8923 (tpp80) cc_final: 0.8692 (mmm-85)
REVERT: A  135 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7979 (tp30)
REVERT: B    1 MET cc_start: 0.2560 (ptt) cc_final: 0.1895 (ppp)
REVERT: B   61 ILE cc_start: -0.0230 (mt) cc_final: -0.0586 (mt)
REVERT: C  304 MET cc_start: 0.8724 (ttp) cc_final: 0.8346 (ttp)
REVERT: C  343 LYS cc_start: 0.8428 (mttt) cc_final: 0.8147 (mtpp)
REVERT: C  443 LEU cc_start: 0.7696 (tp) cc_final: 0.7360 (tt)
REVERT: C  570 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.5266 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 56
  average time/residue: 0.2093
  time to fit residues: 14.8460
Evaluate side-chains
  51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  489 ILE
Chi-restraints excluded: chain C residue  570 TYR
Chi-restraints excluded: chain C residue  571 THR
Chi-restraints excluded: chain C residue  587 TRP
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:    0.5980
   chunk 56 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0370
   chunk 20 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0050
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.4072

-------------------------------------------------------------------------------
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 = 0.3873 r_free = 0.3873 target = 0.119523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.090498 restraints weight = 31629.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.095475 restraints weight = 14868.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.095882 restraints weight = 9001.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3478
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3478
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4983  Z= 0.155
  Angle     :  0.475   7.880   6747  Z= 0.245
  Chirality :  0.040   0.146    737
  Planarity :  0.004   0.034    873
  Dihedral  :  5.834  83.515    664
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.79 %
    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:  1.23 (0.37), residues: 594
  helix:  1.89 (0.34), residues: 262
  sheet:  1.10 (0.58), residues: 88
  loop : -0.46 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 581 
 HIS   0.002   0.001   HIS A  75 
 PHE   0.010   0.001   PHE C 640 
 TYR   0.020   0.001   TYR C 454 
 ARG   0.005   0.000   ARG B  74 

*********************** 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
  53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8315 (tmtt)
REVERT: A  135 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8118 (tp30)
REVERT: B    1 MET cc_start: 0.2157 (ptt) cc_final: 0.1643 (ppp)
REVERT: B   61 ILE cc_start: -0.0547 (mt) cc_final: -0.0902 (mt)
REVERT: C  343 LYS cc_start: 0.8640 (mttt) cc_final: 0.8255 (mtpp)
  outliers start: 7
  outliers final: 5
  residues processed: 53
  average time/residue: 0.2027
  time to fit residues: 13.6939
Evaluate side-chains
  45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  571 THR
Chi-restraints excluded: chain C residue  587 TRP
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:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 21 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 35 optimal weight:    0.1980
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 34 optimal weight:    0.4980
   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 = 0.3861 r_free = 0.3861 target = 0.118798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.088212 restraints weight = 15163.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.091097 restraints weight = 9358.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.093162 restraints weight = 6713.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3447
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4983  Z= 0.189
  Angle     :  0.490   8.461   6747  Z= 0.250
  Chirality :  0.040   0.140    737
  Planarity :  0.004   0.047    873
  Dihedral  :  5.596  86.338    662
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 13.08 %
    Favored  : 85.82 %
  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:  1.22 (0.37), residues: 594
  helix:  1.91 (0.34), residues: 262
  sheet:  1.02 (0.59), residues: 89
  loop : -0.49 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 581 
 HIS   0.003   0.001   HIS A  75 
 PHE   0.008   0.001   PHE C 640 
 TYR   0.020   0.001   TYR C 454 
 ARG   0.003   0.000   ARG B  74 

*********************** 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
  47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.8446 (mtpp) cc_final: 0.8197 (tmtt)
REVERT: A  135 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7959 (tp30)
REVERT: B    1 MET cc_start: 0.4785 (ptt) cc_final: 0.4555 (ppp)
REVERT: C  343 LYS cc_start: 0.8520 (mttt) cc_final: 0.8149 (mtpp)
  outliers start: 6
  outliers final: 6
  residues processed: 47
  average time/residue: 0.2084
  time to fit residues: 12.5676
Evaluate side-chains
  45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  571 THR
Chi-restraints excluded: chain C residue  587 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 14 optimal weight:    8.9990
   chunk 42 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0970
   chunk 54 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 16 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.4356

-------------------------------------------------------------------------------
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 = 0.3868 r_free = 0.3868 target = 0.119210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.090381 restraints weight = 31366.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.095141 restraints weight = 14617.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.095789 restraints weight = 8733.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3476
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3476 r_free = 0.3476    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3476 r_free = 0.3476    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3476
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4983  Z= 0.162
  Angle     :  0.478   9.203   6747  Z= 0.244
  Chirality :  0.040   0.150    737
  Planarity :  0.004   0.042    873
  Dihedral  :  5.618  88.490    662
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.52 %
    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:  1.23 (0.37), residues: 594
  helix:  1.90 (0.34), residues: 262
  sheet:  1.07 (0.59), residues: 89
  loop : -0.48 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 581 
 HIS   0.002   0.001   HIS A  75 
 PHE   0.011   0.001   PHE C 640 
 TYR   0.022   0.001   TYR C 454 
 ARG   0.004   0.000   ARG A 131 

*********************** 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
  50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 LYS cc_start: 0.8291 (mmmm) cc_final: 0.7637 (tttt)
REVERT: A   15 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8300 (tmtt)
REVERT: A  135 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8085 (tp30)
REVERT: C  304 MET cc_start: 0.8716 (ttp) cc_final: 0.8502 (ttp)
REVERT: C  343 LYS cc_start: 0.8652 (mttt) cc_final: 0.8354 (mtpp)
  outliers start: 7
  outliers final: 5
  residues processed: 50
  average time/residue: 0.2204
  time to fit residues: 14.1454
Evaluate side-chains
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  571 THR
Chi-restraints excluded: chain C residue  587 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 56 optimal weight:    0.4980
   chunk 55 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   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 = 0.3859 r_free = 0.3859 target = 0.118391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.086803 restraints weight = 18531.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.090056 restraints weight = 10633.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.092351 restraints weight = 7317.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3434
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3434 r_free = 0.3434    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3434 r_free = 0.3434    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3434
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4983  Z= 0.208
  Angle     :  0.497   9.176   6747  Z= 0.256
  Chirality :  0.040   0.164    737
  Planarity :  0.004   0.053    873
  Dihedral  :  5.658  88.219    662
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.52 %
    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:  0.92 (0.36), residues: 594
  helix:  1.77 (0.34), residues: 268
  sheet:  0.88 (0.61), residues: 84
  loop : -0.83 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 141 
 HIS   0.003   0.001   HIS A  75 
 PHE   0.009   0.001   PHE C 640 
 TYR   0.024   0.001   TYR C 454 
 ARG   0.005   0.000   ARG A 131 

*********************** 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
  49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8224 (tmtt)
REVERT: A  135 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7957 (tp30)
REVERT: C  343 LYS cc_start: 0.8522 (mttt) cc_final: 0.8266 (mtpp)
  outliers start: 6
  outliers final: 5
  residues processed: 49
  average time/residue: 0.2119
  time to fit residues: 13.2130
Evaluate side-chains
  47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  571 THR
Chi-restraints excluded: chain C residue  587 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 7 optimal weight:    0.0870
   chunk 45 optimal weight:    0.5980
   chunk 18 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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 = 0.3862 r_free = 0.3862 target = 0.118585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.088190 restraints weight = 18366.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.092336 restraints weight = 10248.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.092882 restraints weight = 6966.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4983  Z= 0.207
  Angle     :  0.499   9.687   6747  Z= 0.256
  Chirality :  0.040   0.157    737
  Planarity :  0.004   0.058    873
  Dihedral  :  5.631  85.162    662
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 12.52 %
    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:  0.89 (0.36), residues: 594
  helix:  1.76 (0.34), residues: 268
  sheet:  0.89 (0.61), residues: 84
  loop : -0.87 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 141 
 HIS   0.003   0.001   HIS A  75 
 PHE   0.011   0.001   PHE C 640 
 TYR   0.025   0.002   TYR C 454 
 ARG   0.005   0.000   ARG A 131 

*********************** 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
  48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7713 (tttt)
REVERT: A   15 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8278 (tmtt)
REVERT: B    1 MET cc_start: 0.4863 (ppp) cc_final: 0.4611 (ppp)
REVERT: C  304 MET cc_start: 0.8781 (ttp) cc_final: 0.8444 (ttp)
REVERT: C  343 LYS cc_start: 0.8514 (mttt) cc_final: 0.8254 (mtpp)
  outliers start: 5
  outliers final: 5
  residues processed: 48
  average time/residue: 0.2215
  time to fit residues: 13.8004
Evaluate side-chains
  47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  571 THR
Chi-restraints excluded: chain C residue  587 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0060
   chunk 54 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.5596

-------------------------------------------------------------------------------
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 = 0.3866 r_free = 0.3866 target = 0.118891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.088136 restraints weight = 15766.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.091119 restraints weight = 9520.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.093197 restraints weight = 6737.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3448
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3448 r_free = 0.3448    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3448 r_free = 0.3448    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3448
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4983  Z= 0.186
  Angle     :  0.494   9.915   6747  Z= 0.256
  Chirality :  0.040   0.157    737
  Planarity :  0.004   0.059    873
  Dihedral  :  5.552  81.865    662
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 12.52 %
    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:  0.95 (0.36), residues: 594
  helix:  1.71 (0.34), residues: 268
  sheet:  1.02 (0.59), residues: 89
  loop : -0.79 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 141 
 HIS   0.003   0.001   HIS A  75 
 PHE   0.012   0.001   PHE C 640 
 TYR   0.026   0.001   TYR C 454 
 ARG   0.004   0.000   ARG A 139 

********************** 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
  50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 LYS cc_start: 0.8251 (mmmm) cc_final: 0.7679 (tttt)
REVERT: A   15 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8240 (tmtt)
REVERT: B    1 MET cc_start: 0.5843 (ppp) cc_final: 0.5617 (ppp)
REVERT: C  304 MET cc_start: 0.8787 (ttp) cc_final: 0.8446 (ttp)
REVERT: C  343 LYS cc_start: 0.8504 (mttt) cc_final: 0.8247 (mtpp)
  outliers start: 5
  outliers final: 5
  residues processed: 50
  average time/residue: 0.2516
  time to fit residues: 16.9179
Evaluate side-chains
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  571 THR
Chi-restraints excluded: chain C residue  587 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 21 optimal weight:    0.0970
   chunk 53 optimal weight:    0.0040
   chunk 41 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0980
   chunk 11 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 32 optimal weight:    0.1980
   chunk 25 optimal weight:    0.0000
   chunk 36 optimal weight:    0.4980
   overall best weight:    0.0794

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.121506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.087461 restraints weight = 25878.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.091424 restraints weight = 13169.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.094210 restraints weight = 8452.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4983  Z= 0.126
  Angle     :  0.485  10.491   6747  Z= 0.250
  Chirality :  0.039   0.157    737
  Planarity :  0.004   0.060    873
  Dihedral  :  5.271  76.331    662
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 12.71 %
    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:  1.29 (0.37), residues: 594
  helix:  1.91 (0.34), residues: 262
  sheet:  1.18 (0.59), residues: 89
  loop : -0.43 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 141 
 HIS   0.002   0.000   HIS C 371 
 PHE   0.016   0.001   PHE C 640 
 TYR   0.024   0.001   TYR C 454 
 ARG   0.008   0.001   ARG A 139 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 2058.07 seconds
wall clock time: 38 minutes 10.97 seconds (2290.97 seconds total)