Starting phenix.real_space_refine
on Fri Aug 22 15:26:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5a_44205/08_2025/9b5a_44205.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5a_44205/08_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_44205/08_2025/9b5a_44205.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5a_44205/08_2025/9b5a_44205.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5a_44205/08_2025/9b5a_44205.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5a_44205/08_2025/9b5a_44205.cif"
  }
  resolution = 3.65
  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=   0.038
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): 0.01s

  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: 1.87, per 1000 atoms: 0.38
  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: 0.34
  Conformation dependent library (CDL) restraints added in 189.4 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 0.28
  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: 0.54

  Time building geometry restraints manager: 0.46 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:             2.880
  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:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.620
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.770
-------------------------------------------------------------------------------
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      :  0.004   0.106   4985  Z= 0.213
  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 : 4.65
  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 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:  1.20 (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
 ARG   0.003   0.000   ARG C 412 
 TYR   0.011   0.001   TYR A  60 
 PHE   0.010   0.001   PHE C 407 
 TRP   0.009   0.001   TRP C 581 
 HIS   0.005   0.001   HIS C 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4983)
  covalent geometry    : angle       0.47060 ( 6747)
  hydrogen bonds       : bond        0.10494 (  215)
  hydrogen bonds       : angle       5.51580 (  608)
  Misc. bond           : bond        0.07508 (    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
  99 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.212 
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: 0.1050
  time to fit residues: 12.0018
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  : 0.120 
-------------------------------------------------------------------------------
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 54 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3824 r_free = 0.3824 target = 0.115984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.087399 restraints weight = 26747.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.088242 restraints weight = 16758.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.090094 restraints weight = 12511.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.091265 restraints weight = 9151.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.091875 restraints weight = 8132.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3411
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    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 = 0.3409 r_free = 0.3409    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3409
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1886

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= 0.169
  Angle     :  0.560   6.052   6747  Z= 0.290
  Chirality :  0.041   0.136    737
  Planarity :  0.004   0.042    873
  Dihedral  :  5.744  69.626    667
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.23 %
    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:  0.98 (0.36), residues: 594
  helix:  1.85 (0.34), residues: 262
  sheet:  0.60 (0.59), residues: 84
  loop : -0.62 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 139 
 TYR   0.017   0.001   TYR C 454 
 PHE   0.011   0.001   PHE C 622 
 TRP   0.009   0.001   TRP C 581 
 HIS   0.004   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 4983)
  covalent geometry    : angle       0.56002 ( 6747)
  hydrogen bonds       : bond        0.03433 (  215)
  hydrogen bonds       : angle       4.60696 (  608)
  Misc. bond           : bond        0.00223 (    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
  56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.9035 (tpp80) cc_final: 0.8611 (mmm-85)
REVERT: B    1 MET cc_start: 0.2567 (ptt) cc_final: 0.1975 (tmm)
REVERT: B   74 ARG cc_start: 0.7255 (tpp80) cc_final: 0.6823 (mpt180)
REVERT: C  343 LYS cc_start: 0.8506 (mttt) cc_final: 0.8180 (mtpp)
REVERT: C  570 TYR cc_start: 0.6128 (OUTLIER) cc_final: 0.5472 (m-80)
  outliers start: 7
  outliers final: 5
  residues processed: 55
  average time/residue: 0.0921
  time to fit residues: 6.2938
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  : 0.131 
-------------------------------------------------------------------------------
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  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 53 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.117527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.088664 restraints weight = 23917.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.091848 restraints weight = 13188.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.093405 restraints weight = 9153.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.093823 restraints weight = 7153.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.097044 restraints weight = 6232.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3507
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3507
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4985  Z= 0.164
  Angle     :  0.529   5.953   6747  Z= 0.274
  Chirality :  0.041   0.138    737
  Planarity :  0.004   0.039    873
  Dihedral  :  5.931  78.277    664
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 10.68 %
    Favored  : 87.85 %
  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:  0.88 (0.36), residues: 594
  helix:  1.72 (0.34), residues: 262
  sheet:  0.63 (0.59), residues: 83
  loop : -0.64 (0.41), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 139 
 TYR   0.012   0.001   TYR A  60 
 PHE   0.009   0.001   PHE C 622 
 TRP   0.009   0.001   TRP C 581 
 HIS   0.004   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 4983)
  covalent geometry    : angle       0.52916 ( 6747)
  hydrogen bonds       : bond        0.03367 (  215)
  hydrogen bonds       : angle       4.45257 (  608)
  Misc. bond           : bond        0.00016 (    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
  55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.8886 (tpp80) cc_final: 0.8575 (mmm-85)
REVERT: B    1 MET cc_start: 0.2385 (ptt) cc_final: 0.1927 (ppp)
REVERT: B   74 ARG cc_start: 0.7110 (tpp80) cc_final: 0.6860 (mpt180)
REVERT: C  570 TYR cc_start: 0.6075 (OUTLIER) cc_final: 0.5552 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 54
  average time/residue: 0.0882
  time to fit residues: 5.9987
Evaluate side-chains
  50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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 44 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 47 optimal weight:    0.2980
   chunk 45 optimal weight:    0.0030
   chunk 39 optimal weight:    0.2980
   chunk 40 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.3990

-------------------------------------------------------------------------------
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 = 0.118689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.090210 restraints weight = 25739.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.092963 restraints weight = 13690.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.094132 restraints weight = 9611.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.094816 restraints weight = 7330.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.097560 restraints weight = 6625.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3506
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3506 r_free = 0.3506    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3506 r_free = 0.3506    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3506
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4985  Z= 0.112
  Angle     :  0.502   6.122   6747  Z= 0.258
  Chirality :  0.040   0.158    737
  Planarity :  0.004   0.040    873
  Dihedral  :  5.919  79.675    664
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 11.79 %
    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:  0.95 (0.36), residues: 594
  helix:  1.78 (0.34), residues: 262
  sheet:  0.66 (0.59), residues: 84
  loop : -0.62 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 139 
 TYR   0.016   0.001   TYR C 454 
 PHE   0.012   0.001   PHE C 365 
 TRP   0.009   0.001   TRP C 581 
 HIS   0.003   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4983)
  covalent geometry    : angle       0.50179 ( 6747)
  hydrogen bonds       : bond        0.02975 (  215)
  hydrogen bonds       : angle       4.30538 (  608)
  Misc. bond           : bond        0.00097 (    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
  53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.8895 (tpp80) cc_final: 0.8621 (mmm-85)
REVERT: B    1 MET cc_start: 0.2942 (ptt) cc_final: 0.2466 (ppp)
REVERT: B   74 ARG cc_start: 0.7103 (tpp80) cc_final: 0.6869 (mpt180)
REVERT: C  570 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.5492 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 51
  average time/residue: 0.1031
  time to fit residues: 6.5646
Evaluate side-chains
  48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain B residue   12 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0970
   chunk 18 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 52 optimal weight:    0.4980
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.117678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.086702 restraints weight = 18206.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.089714 restraints weight = 11020.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.091838 restraints weight = 7770.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.093363 restraints weight = 6044.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.094420 restraints weight = 5017.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
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 = 0.36   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 = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4985  Z= 0.148
  Angle     :  0.521   8.134   6747  Z= 0.266
  Chirality :  0.040   0.143    737
  Planarity :  0.004   0.038    873
  Dihedral  :  5.992  82.491    664
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.79 %
    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 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:  0.74 (0.36), residues: 594
  helix:  1.64 (0.34), residues: 268
  sheet:  0.68 (0.59), residues: 84
  loop : -0.90 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 139 
 TYR   0.019   0.002   TYR C 454 
 PHE   0.009   0.001   PHE C 622 
 TRP   0.008   0.001   TRP C 581 
 HIS   0.004   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4983)
  covalent geometry    : angle       0.52148 ( 6747)
  hydrogen bonds       : bond        0.03050 (  215)
  hydrogen bonds       : angle       4.31830 (  608)
  Misc. bond           : bond        0.00010 (    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
  57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4840 (ptt) cc_final: 0.4222 (ppp)
REVERT: B   74 ARG cc_start: 0.7288 (tpp80) cc_final: 0.6921 (mpt180)
REVERT: C  570 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.5395 (m-80)
  outliers start: 10
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0907
  time to fit residues: 6.1445
Evaluate side-chains
  49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
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  576 ILE
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 35 optimal weight:    0.0870
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0980
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 4 optimal weight:    0.1980
   overall best weight:    0.3558

-------------------------------------------------------------------------------
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 = 0.3865 r_free = 0.3865 target = 0.119047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.090787 restraints weight = 23842.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.093711 restraints weight = 12414.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.095530 restraints weight = 7961.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.094899 restraints weight = 6340.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.096465 restraints weight = 5664.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3490 r_free = 0.3490    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 = 0.3490 r_free = 0.3490    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3490
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   4985  Z= 0.099
  Angle     :  0.480   7.834   6747  Z= 0.248
  Chirality :  0.039   0.147    737
  Planarity :  0.004   0.045    873
  Dihedral  :  5.928  85.140    664
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.79 %
    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:  0.95 (0.36), residues: 594
  helix:  1.69 (0.34), residues: 269
  sheet:  1.07 (0.58), residues: 87
  loop : -0.78 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 139 
 TYR   0.021   0.001   TYR C 454 
 PHE   0.008   0.001   PHE C 365 
 TRP   0.008   0.001   TRP C 581 
 HIS   0.002   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 4983)
  covalent geometry    : angle       0.48007 ( 6747)
  hydrogen bonds       : bond        0.02697 (  215)
  hydrogen bonds       : angle       4.14959 (  608)
  Misc. bond           : bond        0.00023 (    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
  55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ARG cc_start: 0.7489 (ttp80) cc_final: 0.6454 (ttp80)
  outliers start: 9
  outliers final: 8
  residues processed: 55
  average time/residue: 0.0808
  time to fit residues: 5.6146
Evaluate side-chains
  47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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   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  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 7 optimal weight:    0.0570
   chunk 50 optimal weight:    0.0050
   chunk 42 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 11 optimal weight:    0.1980
   chunk 2 optimal weight:    7.9990
   chunk 12 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 45 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0270
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.1170

-------------------------------------------------------------------------------
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 = 0.3883 r_free = 0.3883 target = 0.120246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.090675 restraints weight = 23721.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.095026 restraints weight = 12499.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.098126 restraints weight = 7535.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.098276 restraints weight = 5545.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.098802 restraints weight = 4570.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3534
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3534 r_free = 0.3534    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3534 r_free = 0.3534    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3534
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4985  Z= 0.091
  Angle     :  0.473   7.594   6747  Z= 0.248
  Chirality :  0.039   0.158    737
  Planarity :  0.004   0.040    873
  Dihedral  :  5.606  88.904    662
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.71 %
    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 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:  1.27 (0.36), residues: 594
  helix:  1.88 (0.34), residues: 263
  sheet:  1.19 (0.59), residues: 87
  loop : -0.42 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 139 
 TYR   0.023   0.001   TYR C 454 
 PHE   0.009   0.001   PHE C 365 
 TRP   0.037   0.002   TRP A 141 
 HIS   0.002   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 4983)
  covalent geometry    : angle       0.47271 ( 6747)
  hydrogen bonds       : bond        0.02627 (  215)
  hydrogen bonds       : angle       4.00345 (  608)
  Misc. bond           : bond        0.00017 (    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
  51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7600 (tttt)
REVERT: A   15 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8120 (tmtt)
  outliers start: 6
  outliers final: 6
  residues processed: 50
  average time/residue: 0.0867
  time to fit residues: 5.5056
Evaluate side-chains
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0970
   chunk 31 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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 = 0.3858 r_free = 0.3858 target = 0.118612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.090017 restraints weight = 11583.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.092412 restraints weight = 7745.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.094053 restraints weight = 5834.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.095284 restraints weight = 4769.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.096147 restraints weight = 4103.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2725

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= 0.125
  Angle     :  0.481   7.348   6747  Z= 0.250
  Chirality :  0.040   0.139    737
  Planarity :  0.004   0.053    873
  Dihedral  :  5.573  86.401    662
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.15 %
    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:  1.07 (0.36), residues: 594
  helix:  1.77 (0.34), residues: 269
  sheet:  1.21 (0.60), residues: 87
  loop : -0.71 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 131 
 TYR   0.023   0.001   TYR C 454 
 PHE   0.008   0.001   PHE C 622 
 TRP   0.024   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4983)
  covalent geometry    : angle       0.48067 ( 6747)
  hydrogen bonds       : bond        0.02800 (  215)
  hydrogen bonds       : angle       4.07671 (  608)
  Misc. bond           : bond        0.00028 (    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
  47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5620 (ppp) cc_final: 0.5376 (ppp)
  outliers start: 7
  outliers final: 6
  residues processed: 47
  average time/residue: 0.0808
  time to fit residues: 4.9217
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  : 0.183 
-------------------------------------------------------------------------------
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0980
   chunk 2 optimal weight:    8.9990
   chunk 56 optimal weight:    0.0970
   chunk 51 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 53 optimal weight:    0.3980
   overall best weight:    0.3778

-------------------------------------------------------------------------------
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 = 0.3872 r_free = 0.3872 target = 0.119521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.087900 restraints weight = 18650.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.091234 restraints weight = 10648.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.093563 restraints weight = 7284.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.095080 restraints weight = 5567.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.096306 restraints weight = 4617.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3499
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3499
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4985  Z= 0.100
  Angle     :  0.480   7.506   6747  Z= 0.250
  Chirality :  0.040   0.167    737
  Planarity :  0.004   0.057    873
  Dihedral  :  5.525  84.667    662
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.15 %
    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:  1.05 (0.36), residues: 594
  helix:  1.72 (0.34), residues: 269
  sheet:  1.21 (0.59), residues: 87
  loop : -0.70 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 139 
 TYR   0.024   0.001   TYR C 454 
 PHE   0.008   0.001   PHE C 365 
 TRP   0.021   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 4983)
  covalent geometry    : angle       0.48014 ( 6747)
  hydrogen bonds       : bond        0.02693 (  215)
  hydrogen bonds       : angle       4.02216 (  608)
  Misc. bond           : bond        0.00080 (    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
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 LYS cc_start: 0.8210 (mmmm) cc_final: 0.7665 (tttt)
REVERT: B    1 MET cc_start: 0.5652 (ppp) cc_final: 0.5401 (ppp)
  outliers start: 6
  outliers final: 6
  residues processed: 46
  average time/residue: 0.0830
  time to fit residues: 4.8659
Evaluate side-chains
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0870
   chunk 52 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0870
   chunk 57 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0020
   overall best weight:    0.3144

-------------------------------------------------------------------------------
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 = 0.3872 r_free = 0.3872 target = 0.119535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.087602 restraints weight = 19309.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.090924 restraints weight = 10971.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.093306 restraints weight = 7498.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.094939 restraints weight = 5697.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.096120 restraints weight = 4687.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3499
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3499
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4985  Z= 0.093
  Angle     :  0.469   7.513   6747  Z= 0.244
  Chirality :  0.039   0.159    737
  Planarity :  0.004   0.059    873
  Dihedral  :  5.469  83.336    662
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.15 %
    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:  1.08 (0.36), residues: 594
  helix:  1.76 (0.34), residues: 269
  sheet:  1.23 (0.59), residues: 87
  loop : -0.70 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 139 
 TYR   0.024   0.001   TYR C 454 
 PHE   0.008   0.001   PHE C 365 
 TRP   0.020   0.001   TRP A 141 
 HIS   0.002   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 4983)
  covalent geometry    : angle       0.46935 ( 6747)
  hydrogen bonds       : bond        0.02654 (  215)
  hydrogen bonds       : angle       4.01373 (  608)
  Misc. bond           : bond        0.00025 (    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
  47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 LYS cc_start: 0.8214 (mmmm) cc_final: 0.7669 (tttt)
REVERT: A   15 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7995 (tmtt)
REVERT: B    1 MET cc_start: 0.5795 (ppp) cc_final: 0.5548 (ppp)
  outliers start: 6
  outliers final: 6
  residues processed: 46
  average time/residue: 0.0669
  time to fit residues: 4.0045
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  : 0.192 
-------------------------------------------------------------------------------
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 2 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0010
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.5986

-------------------------------------------------------------------------------
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 = 0.118768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.088057 restraints weight = 15965.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.091018 restraints weight = 9673.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.093091 restraints weight = 6867.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.094562 restraints weight = 5385.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.095423 restraints weight = 4510.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3488
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3488
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2787

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= 0.119
  Angle     :  0.476   7.323   6747  Z= 0.247
  Chirality :  0.040   0.157    737
  Planarity :  0.004   0.060    873
  Dihedral  :  5.457  82.048    662
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.15 %
    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:  1.06 (0.36), residues: 594
  helix:  1.77 (0.34), residues: 269
  sheet:  1.23 (0.60), residues: 87
  loop : -0.74 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 139 
 TYR   0.025   0.001   TYR C 454 
 PHE   0.008   0.001   PHE C 622 
 TRP   0.018   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4983)
  covalent geometry    : angle       0.47559 ( 6747)
  hydrogen bonds       : bond        0.02725 (  215)
  hydrogen bonds       : angle       4.06554 (  608)
  Misc. bond           : bond        0.00019 (    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: 994.76 seconds
wall clock time: 17 minutes 34.15 seconds (1054.15 seconds total)